Cis-prenyltransferases from the rubber-producing plants russian dandelion (taraxacum kok-saghyz) and sunflower (helianthus annus)

ABSTRACT

This invention pertains to nucleic acid fragments encoding plant cis-prenyltransferases. More specifically, this invention pertains to a cis-prenyltransferase homolog from latex of the rubber-producing plant species  Taraxacum kok - saghyz  (russian dandelion) and a cis-prenyltransferase homolog from the rubber-producing plant species  Helianthus annus  (sunflower).

FIELD OF THE INVENTION

This invention is in the field of plant molecular biology. More specifically, this invention pertains to the identification of cis-prenyltransferase genes preferentially expressed in the rubber-producing plants Taraxacum kok-saghyz (russian dandelion) and Helianthus annus (sunflower) and their utility in altering natural rubber production in transgenic plants.

BACKGROUND OF THE INVENTION

Natural rubber (cis-1,4-polyisoprene) is produced in about 2000 plant species (usually as a constituent of plant latex) with varying degrees of quality and quantity. Several well-studied examples of rubber-producing plants include:

-   -   1. Indian laurel (Ficus elastica), a well-known household plant         that produces a rubber-containing latex.     -   2. Trees of the Sapotacae family (Palaquim gutta and P.         oblongifolia), located in the Malaysian peninsula and         responsible for gutta percha latex (a viscous, grayish latex         that exudes slowly from cuts in the bark and rapidly turns brown         after exposure to the air).     -   3. The tropical American tree Mimusops balata, which produces         Balata latex as white or reddish exudates.     -   4. The tropical American saprodilla tree Archras zapote, which         produces Chicle     -   5. The Central American tree Castilla elastica, which produces         caucho negro rubber.     -   6. The Brazilian species, Manihot glazovii, which produces ceara         rubber.     -   7. The dandelion species kok-saghyz (Taraxacum kok-saghyz; from         Kazakhstan) and krim-saghyz (T. megalorhizon; found in the         Crimea and throughout the Mediterranean region), which produce a         high-quality rubber in their roots.     -   8. The non-latex producing American desert shrub guayule         (Parthenium argentatum), in which rubber is produced seasonally         within parenchymatous cells of the stem and root, and its         isolation requires harvesting of the plant and maceration of the         tissue.         The natural rubbers produced by each of these species differ in         one or more of their properties. In particular, differences in         molecular weight and molecular weight distribution have been         observed in natural rubbers depending on their plant origin         (Backhaus, R. A. Israel Journal of Botany 34: 283-293 (1985)).

Natural rubber, despite the development of many synthetic polymer alternatives, remains a high-volume commodity material based on its supeior properties of elasticity, resilience, and resistence to high temperature. Currently, some 6,810,000 tons of natural rubber are produced annually. Despite this abundance, latex tapped from the tree Hevea brasiliensis is today the only significant commercial source of natural rubber and it is expected that global demand will soon be greater than supplies. Thus, there is significant interest in studying rubber biosynthesis and the differences between rubber produced by Hevea to other natural rubbers, in order to develop alternative rubbersources. In particular, it would be useful to industry to have available rubbers with different molecular weight averages (higher and lower than Hevea rubber) and distributions. For example, rubbers with molecular weights lower than those obtained from H. brasiliensis may have distinct advantages over the Hevea material in certain applications due to their ease of processing (Nor, H. M., and Ebdon, J. R. Progress in Polymer Sci. 23: 143-177 (1998); Meeker, T. Low Molecular Weight Polyisoprenes Offer Versatility In Bonding Techniques. Adhesives Age; pp. 23-26 (July 1998)). Although the molecular weights of rubbers synthesized in in vitro experiments with isolated, enzymatically-active rubber particles are highly influenced by the concentrations of initiator allylic diphosphate and isopentenyl diphosphate (IPP), the intrinsic properties of the cis-prenyltransferases themselves also play a role in determining the size of the rubber molecules they produce (Cornish, K. Phytochemistry 57: 1123-1134 (2001)).

Cis-prenyltransferases are a family of enzymes that are responsible for synthesizing natural rubbers, by catalyzing the sequential addition of C₅ units (in the form of isopentenyl pyrophosphate (IPP)) to an initiator molecule in head-to-tail condensation reactions. The initiator molecules themselves are derived from isoprene units through the action of distinct prenyltransferases. These initiators are allylic terpenoid diphosphates such as dimethylallyldiphosphate (DMAPP; C₅), geranyl diphosphate (GPP; C₁₀), farnesyl diphosphate (FPP; C₁₅), and geranylgeranyl diphosphate (GGPP; C₂₀). Genes encoding the enzymes which synthesize these allylic terpenoid diphosphates have been cloned from a number of organisms, including plants, and all of these genes encode polypeptides with conserved regions of homology (McGarvey et al., Plant Cell 7:1015-1026 (1995); Chappell, J., Annu. Rev. Plant Physiol. Plant Mol. Biol. 46:521-547 (1995)). All of these gene products condense isoprene units in the trans- configuration. Prenyltransferases that condense isoprene units in a cis-configuration have only recently been identified in microbes and plants. Most notable to the present disclosure herein is the discovery of cis-prenyltransferase gene products in latex of the rubber-producing species Hevea brasiliensis (WO01/21650; GenBank Accession Numbers AY124934, AY124474, AY124473, AY124472, AY124471, AY124470, AY124469, AY124468, AY124467, AY124466, AY124465, AY124464; see also AB061236 and AB074307).

In the present disclosure, the problem to be solved therefore is to identify new plant cis-prenyltransferase genes. These genes will have utility in modification of the properties of natural rubbers obtained from plants. Applicants have solved the stated problem by identifying plant genes encoding cis-prenyltransferases from rubber-producing russian dandelion and sunflower species (both of which produce natural rubbers with different properties than those obtained from H. brasiliensis). Additionally, Applicants have discovered diagnostic features within the gene sequences of cis-prenyltransferases from rubber-producing species.

SUMMARY OF THE INVENTION

Accordingly the invention provides an isolated nucleic acid molecule encoding a cis-prenyltransferase enzyme, selected from the group consisting of:

-   -   a) an isolated nucleic acid molecule encoding the amino acid         sequence as set forth in SEQ ID NOs:4 and 6;     -   b) an isolated nucleic acid molecule that hybridizes with (a)         under the following hybridization conditions: 0.1×SSC, 0.1% SDS,         65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1%         SDS; or     -   an isolated nucleic acid molecule that is complementary to (a)         or (b).

Specifically the invention provides an isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 301 amino acids that has at least 70% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO:4 or a second nucleotide sequence comprising the complement of the first nucleotide sequence, wherein said enzyme has cis-prenyltransferase activity.

In similar fashion the invention provides An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 168 amino acids that has at least 70% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO:6 or a second nucleotide sequence comprising the complement of the first nucleotide sequence, wherein said enzyme has cis-prenyltransferase activity.

Additionally the invention provides polypeptides encoded by the isolated nucleic acid molecules of the invention as well as genetic chimera constructed therefrom and recombinant host cells containing and expressing the same.

In another embodiment the invention provides a method of obtaining a nucleic acid molecule encoding a cis-prenyltransferase enzyme comprising:

-   -   a) probing a genomic library with the nucleic acid molecule of         the invention;     -   b) identifying a DNA clone that hybridizes with the nucleic acid         molecule of the invention;     -   c) sequencing the genomic fragment that comprises the clone         identified in step (b),     -   wherein the sequenced genomic fragment encodes a         cis-prenyltransferase enzyme.

In similar fashion the invention provides a method of obtaining a nucleic acid molecule encoding a cis-prenyltransferase enzyme comprising:

-   -   a) synthesizing at least one oligonucleotide primer         corresponding to a portion of the sequence selected from the         group consisting of SEQ ID NOs:3 and 5; and     -   b) amplifying an insert present in a cloning vector using the         oligonucleotide primer of step (a);     -   wherein the amplified insert encodes a portion of an amino acid         sequence encoding a cis-prenyltransferase enzyme.

In a preferred embodiment the invention provides a method of altering the level of expression of a plant cis-prenyltransferase protein in a host cell comprising:

-   -   (a) transforming a host cell with the chimeric gene of the         invention and;     -   (b) growing the transformed host cell produced in step (a) under         conditions that are suitable for expression of the chimeric gene         resulting in production of altered levels of a plant         cis-prenyl-transferase protein in the transformed host cell         relative to expression levels of an untransformed host cell.

In a preferred embodiment the invention provides a method for the production of natural rubber compounds comprising:

-   -   a) providing a transformed host cell comprising:         -   (i) suitable levels of isopentenyl pyrophate; and         -   (ii) a cis-prenyltransferase gene selected from the group             consisting of SEQ ID NOs: 3 and 5, wherein said genes are             operably linked to suitable regulatory sequences; and     -   b) growing the transformed host cell of (a) under conditions         whereby a natural rubber compound is produced.

Similarly the invention provides a method for the identification of a polypeptide having cis-prenyltransferase activity in a rubber-producing plant comprising:

-   -   (a) obtaining the amino acid sequence of a polypeptide suspected         of having cis-prenyltransferase activity; and     -   (b) aligning the amino acid sequence of step (a) with the amino         acid sequence of a cis-prenyltransferase consensus sequence         selected from the group consisting of SEQ ID NO:4, 6, 8, 9, and         10, wherein the alignment shows the presence of conserved         domains I, IV, and V (SEQ ID NOs: 38-40).

In an alternate embodiment the invention provides a method for the identification of a polypeptide having cis-prenyltransferase activity in a rubber-producing plant comprising:

-   -   (a) obtaining the amino acid sequence of a polypeptide suspected         of having cis-prenyltransferase activity; and     -   (b) aligning the amino acid sequence of step (a) with the amino         acid sequence of a cis-prenyltransferase consensus sequence         selected from the group consisting of SEQ ID NO:4, 6, 8, 9, and         10, wherein the alignment shows a sequence of at least about 50         non-conserved amino acids present between the absolutely         conserved tyrosine of Domain IV and the first of the absolutely         conserved arginine residue of Domain V.

BRIEF DESCRIPTION OF THE DRAWINGS AND SEQUENCE DESCRIPTIONS

FIG. 1 shows an alignment of the regions between Domains IV and V of cis-prenyltransferases from rubber-producing plants (i.e., russian dandelion, sunflower and Hevea) and non-rubber-producing plants and microbes.

FIG. 2 shows the analysis of expression of the russian dandelion cis-prenyltransferase gene by Northern blotting.

The invention can be more fully understood from the following detailed description and the accompanying sequence descriptions, which form a part of this application.

The following sequences comply with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPO and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.

SEQ ID NOs:1-34, 38-40 and 45 are genes or proteins as identified 25 in Table 1. TABLE 1 Summary of Gene and Protein SEQ ID Numbers SEQ ID Clone ID number and Nucleic SEQ ID Description Organism acid Peptide EST etk1c.pk006.a10 Taraxacum kok-saghyz 1 — (russian dandelion) 5′RACE product #3-4 Taraxacum kok-saghyz 2 — (russian dandelion) full-length nucleotide Taraxacum kok-saghyz 3 4 sequence for cis- (russian dandelion) prenyltransferase (assembled from SEQ ID NO: 1 and SEQ ID NO: 2) hls1c.pk020.m9 Helianthus annus 5 6 (sunflower) ecs1c.pk009.p19 Calendula officinalis — 7 (pot marigold) ehb2c.pk001.i10 Hevea brasiliensis — 8 ehb2c.pk001.d17 Hevea brasiliensis — 9 ehb2c.pk001.o18 Hevea brasiliensis — 10 vdb1c.pk001.k23 Vitis sp. (grape) — 11 r10n.pk117.i23 Oryza sativa (rice) — 12 rr1.pk0050.h8 Oryza sativa (rice) — 13 sl1.pk0128.h7 Glycine max (soybean) — 14 wdk5c.pk005.f22 Triticum aestivum — 15 (wheat) ecs1c.pk009.p19 Dimorphotheca sinuata — 16 (african daisy) bacterial undecaprenyl Micrococcus luteus 17 18 diphosphate synthase undecaprenyl Saccharomyces 19 20 phosphate synthase cerevisiae, strain rer2 undecaprenyl Saccharomyces 21 22 phosphate synthase cerevisiae, strain srt1 MUF9.18 Arabidopsis (Genbank — 23 Accession No. NM_125443) MJB20.13 Arabidopsis (Genbank — 24 Accession No. NM_127311) F26B6.6 Arabidopsis (Genbank — 25 Accession No. NM_127905) MZN1.22 Arabidopsis (Genbank — 26 Accession No. NM_125267) conserved Domain IV alignment consensus — 27 sequence conserved Domain V alignment consensus — 28 sequence conserved Domain I consensus sequence — 29 from Apfel et al. (J. Bact. 182(2): 483-492 (1999)) conserved Domain II consensus sequence — 30 from Apfel et al. (supra) conserved Domain III consensus sequence — 31 from Apfel et al. (supra) conserved Domain IV consensus sequence — 32 from Apfel et al. (supra) conserved Domain V consensus sequence — 33 from Apfel et al. (supra) Conserved Domain V Consensus sequence — 34 from Taraxacum kok- saghyz (russian dandelion) and Helianthus annus (sunflower) ESTs conserved Domain I consensus sequence — 38 in rubber-producing species conserved Domain IV consensus sequence — 39 in rubber-producing species conserved Domain V consensus sequence — 40 in rubber-producing species Clone #4-4 Taraxacum kok-saghyz — 45 (RT-PCR product) (russian dandelion) latex

SEQ ID NOs:41 and 42 are the primers Dan5 and Dan6.

SEQ ID NOs: 36, 37, and 44 are the primers NKH46, NKH45, and NKH5.

SEQ ID NO:43 is the primer DegHptS.

SEQ ID NO:35 is the peptide ‘ELVISLIVES’.

DETAILED DESCRIPTION OF THE INVENTION

The present invention reports the isolation and characterization of cDNAs corresponding to cis-prenyltransferases from russian dandelion and sunflower. Applications for these genes include the development of novel plant phenotypes possessing greater plant defense responses, crop production, and/or creation of industrial sources of polyisoprenoids (including natural rubber). Furthermore, the present invention provides a technique for readily identifying other cis-prenyltransferase genes from rubber-producing plants.

Definitions

The following definitions are provided for the full understanding of terms and abbreviations used in this specification:

“Polymerase chain reaction” is abbreviated PCR.

“Open reading frame” is abbreviated ORF.

“Expressed sequence tag” is abbreviated EST.

“SDS polyacrylamide gel electrophoresis” is abbreviated SDS-PAGE.

“UPPS” is the abbreviation for the specific undecaprenyl diphosphate synthases isolated from bacteria.

“Dimethyl allyl diphosphate” is abbreviated DMAPP.

“Isopentenyl diphosphate” is abbreviated IPP.

“Geranyl diphosphate” is abbreviated GPP.

“Famesyl diphosphate” is abbreviated FPP.

“Geranylgeranyl diphosphate” is abbreviated GGPP.

“Polyisoprenoids” refer to a variety of hydrocarbons produced by plants that are built up of isoprene units (C₅H₈) (Tanaka, Y. In Rubber and Related Polyprenols. Methods in Plant Biochemistry, Dey, P. M. and Harborne, J. B., Eds., Academic Press: San Diego, 1991; Vol. 7, pp 519-536). Those with 45 to 115 carbon atoms and varying numbers of cis- and trans- (Z- and E-) double bonds are termed “polyprenols”, while those polyisoprenoids of longer chain length are termed natural “rubbers” (Tanaka, Y. In Minor Classes of Terpenoids. Methods in Plant Biochemistry; Dey, P. M. and Harborne, J. B., Eds., Academic: San Diego, 1991; Vol. 7, pp 537-542). There are several-suggested functions for plant polyisoprenoids. For example, terpenoid quinones are most likely involved in photophosphorylation and respiratory chain phosphorylation, while rubbers have been implicated in plant defense against herbivory, by possibly serving to repel and entrap insects and seal wounds in a manner analogous to plant resins. The specific roles of the C₄₅-C₁₁₅ polyprenols, however, remain unidentified (although as with most secondary metabolites they too most likely function in plant defense). Short-chain polyprenols may also be involved in protein glycosylation in plants, by analogy with the role of dolichols in animal metabolism.

The term “rubber” encompasses any material that is highly elastic; i.e., the elastic material can be stretched without breaking and will return to its original length on removal of the stretching force. “Natural rubbers” are those rubbers produced by plant species, often (though not always) as a constituent of latex.

The term “plant latex” refers to a milky fluid present in lacticifers, or latex ducts, which seeps out of the plant upon wounding.

The term “cis-prenyltransferase” refers generally to a class of enzymes capable of catalyzing the sequential addition of C₅ units to polyprenols and rubbers in cis 1-4 orientation. Two examples of cis-prenyltransferases are the undecaprenyl diphosphate and dehydrodolichyl diphosphate synthase.

The term “initiator molecules” or “initiators” refers to allylic terpenoid diphosphates that are derived from isoprene units (IPP) through the action of prenyltransferases. Examples of common initiators include: dimethylallyldiphosphate (DMAPP), a C₅ compound; geranyl diphosphate (GPP), a C₁₀ compound; farnesyl diphosphate (FPP), a C₁₅ compound; and, geranylgeranyl diphosphate (GGPP), a C₂₀ compound.

The term “plant defense response” refers to the ability of a plant to deter tissue damage by insects, pathogens (e.g., fungi, bacteria or viruses), and/or herbivores.

As used herein, an “isolated nucleic acid fragment” is a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid fragment in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.

The term “fragment” refers to a DNA or amino acid sequence comprising a subsequence of the nucleic acid sequence or protein of the present invention. However, an active fragment of the present invention comprises a sufficient portion of the protein to maintain activity.

A nucleic acid molecule is “hybridizable” to another nucleic acid molecule, such as a cDNA, genomic DNA, or RNA molecule, when a single stranded form of the nucleic acid molecule can anneal to the other nucleic acid molecule under the appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known and exemplified in Sambrook, J., Fritsch, E. F. and Maniatis, T. (Molecular Cloning: A Laboratory Manual, 2^(nd) ed.; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1989 (hereinafter “Maniatis”), particularly Chapter 11 and Table 11.1 therein (entirely incorporated herein by reference). The conditions of temperature and ionic strength determine the “stringency” of the hybridization. Stringency conditions can be adjusted to screen for moderately similar fragments (such as homologous sequences from distantly related organisms), to highly similar fragments (such as genes that duplicate functional enzymes from closely related organisms). Post-hybridization washes determine stringency conditions. One set of preferred conditions uses a series of washes starting with 6×SSC, 0.5% SDS at room temperature for 15 min, then repeated with 2×SSC, 0.5% SDS at 45° C. for 30 min, and then repeated twice with 0.2×SSC, 0.5% SDS at 50° C. for 30 min. A more preferred set. of stringent conditions uses higher temperatures in which the washes are identical to those above except for the temperature of the final two 30 min washes in 0.2×SSC, 0.5% SDS was increased to 60° C. Another preferred set of highly stringent conditions uses two final washes in 0.1×SSC, 0.1% SDS at 65° C. An additional set of stringent conditions include hybridization at 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS, for example.

Hybridization requires that the two nucleic acids contain complementary sequences, although depending on the stringency of the hybridization, mismatches between bases are possible. The appropriate stringency for hybridizing nucleic acids depends on the length of the nucleic acids and the degree of complementation, variables well known in the art. The greater the degree of similarity or homology between two nucleotide sequences, the greater the value of Tm for hybrids of nucleic acids having those sequences. The relative stability (corresponding to higher Tm) of nucleic acid hybridizations decreases in the following order: RNA:RNA, DNA:RNA, DNA:DNA. For hybrids of greater than 100 nucleotides in length, equations for calculating Tm have been derived (see Maniatus, supra, 9.50-9.51). For hybridizations with shorter nucleic acids, i.e., oligonucleotides, the position of mismatches becomes more important, and the length of the oligonucleotide determines its specificity (see Maniatus, supra, 11.7-11.8). In one embodiment the length for a hybridizable nucleic acid is at least about 10 nucleotides. Preferably a minimum length for a hybridizable nucleic acid is at least about 15 nucleotides; more preferably at least about 20 nucleotides; and most preferably the length is at least 30 nucleotides. Furthermore, the skilled artisan will recognize that the temperature and wash solution salt concentration may be adjusted as necessary according to factors such as length of the probe.

A “substantial portion” of an amino acid or nucleotide sequence is that portion comprising enough of the amino acid sequence of a polypeptide or the nucleotide sequence of a gene to putatively identify that polypeptide or gene, either by manual evaluation of the sequence by one skilled in the art, or by computer-automated sequence comparison and identification using algorithms such as BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., J. Mol. Biol. 215:403-410 (1993); see also www.ncbi.nlm.nih.gov/BLAST/). In general, a sequence of ten or more contiguous amino acids or thirty or more nucleotides is necessary in order to putatively identify a polypeptide or nucleic acid sequence as homologous to a known protein or gene. Moreover, with respect to nucleotide sequences, gene specific oligonucleotide probes comprising 20-30 contiguous nucleotides may be used in sequence-dependent methods of gene identification (e.g., Southern hybridization) and isolation (e.g., in situ hybridization of bacterial colonies or bacteriophage plaques). In addition, short oligonucleotides of 12-15 bases may be used as amplification primers in PCR in order to obtain a particular nucleic acid fragment comprising the primers. Accordingly, a “substantial portion” of a nucleotide sequence comprises enough of the sequence to specifically identify and/or isolate a nucleic acid fragment comprising the sequence. The instant specification teaches partial or complete amino acid and nucleotide sequences encoding one or more particular plant proteins. The skilled artisan, having the benefit of the sequences as reported herein, may now use all or a substantial portion of the disclosed sequences for purposes known to those skilled in this art Accordingly, the instant invention comprises the complete sequences as reported in the accompanying Sequence Listing, as well as substantial portions of those sequences as defined above.

The term “complementary” is used to describe the relationship between nucleotide bases that are capable of hybridizing to one another. For example, with respect to DNA, adenosine is complementary to thymine and cytosine is complementary to guanine. Accordingly, the instant invention also includes isolated nucleic acid fragments that are complementary to the complete sequences as reported in the accompanying Sequence Listing as well as those substantially similar nucleic acid sequences.

The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between polypeptide or polynucleotide sequences, as the case may be, as determined by the match between strings of such sequences. “Identity” and “similarity” can be readily calculated by known methods, including (but not limited to) those described in: 1.) Computational Molecular Biology; Lesk, A. M., Ed.; Oxford University: N.Y., 1988; 2.) Biocomputing: Informatics and Genome Projects; Smith, D. W., Ed.; Academic: N.Y., 1993; 3.) Computer Analysis of Sequence Data, Part I; Griffin, A. M., and Griffin, H. G., Eds.; Humana: N.J., 1994; 4.) Sequence Analysis in Molecular Biology; von Heinje, G., Ed.; Academic, 1987; and 5.) Sequence Analysis Primer; Gribskov, M. and Devereux, J., Eds.; Stockton: N.Y., 1991. Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the AlignX program of the Vector NTI bioinformatics computing suite (InforMax Inc., North Bethesda, Md.). Multiple alignment of the sequences was performed using the Clustal method of alignment (Higgins and Sharp CABIOS. 5:151-153 (1989)) with the default parameters (GAP OPENING PENALTY=10, GAP EXTENSION PENALTY=0.1). Default parameters for pairwise alignments using the Clustal method were KTUPLE SIZE=1, GAP PENALTY=3, WINDOW SIZE=5 and NUMBER OF BEST DIAGONALS=5.

Suitable nucleic acid fragments (isolated polynucleotides of the present invention) encode polypeptides that are at least about 70% identical, preferably at least about 80% identical to the amino acid sequences reported herein. Preferred nucleic acid fragments encode amino acid sequences that are about 85% identical to the amino acid sequences reported herein. More preferred nucleic acid fragments encode amino acid sequences that are at least about 90% identical to the amino acid sequences reported herein. Most preferred are nucleic acid fragments that encode amino acid sequences that are at least about 95% identical to the amino acid sequences reported herein. Suitable nucleic acid fragments not only have the above homologies but typically encode a polypeptide having at least 50 amino acids, preferably at least 100 amino acids, more preferably at least 150 amino acids, still more preferably at least 200 amino acids, and most preferably at least 250 amino acids.

“Codon degeneracy” refers to the divergence in the genetic code permitting variation of the nucleotide sequence without effecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment that encodes all or a substantial portion of the amino acid sequence encoding the instant plant polypeptides as set forth in SEQ ID NOs:4 and 6. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.

“Synthetic genes” can be assembled from oligonucleotide building blocks that are chemically synthesized using procedures known to those skilled in the art. These building blocks are ligated and annealed to form gene segments that are then enzymatically assembled to construct the entire gene. “Chemically synthesized”, as related to a sequence of DNA, means that the component nucleotides were assembled in vitro. Manual chemical synthesis of DNA may be accomplished using well-established procedures, or automated chemical synthesis can be performed using one of a number of commercially available machines. Accordingly, the genes can be tailored for optimal gene expression based on optimization of nucleotide sequence to reflect the codon bias of the host cell. The skilled artisan appreciates the likelihood of successful gene expression if codon usage is biased towards those codons favored by the host. Determination of preferred codons can be based on a survey of genes derived from the host cell where sequence information is available.

“Gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences. “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. “Endogenous gene” refers to a native gene in its natural location in the genome of an organism. A “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. A “transgene” is a gene that has been introduced into the genome by a transformation procedure.

“Coding sequence” refers to a DNA sequence that codes for a specific amino acid sequence. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ non-coding sequences), within, or downstream (3′ non-coding sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding site and stem-loop structure.

“Promoter” refers to a DNA sequence capable of controlling the expression of a coding sequence or functional RNA. In general, a coding sequence is located 3′ to a promoter sequence. Promoters may be derived in their entirety from a native gene, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is understood by those skilled in the art that different promoters may direct the expression of a gene in different tissues or cell types, or at different stages of development, or in response to different environmental or physiological conditions. Promoters which cause a gene to be expressed in most cell types at most times are commonly referred to as “constitutive promoters”. It is further recognized that since in most cases the exact boundaries of regulatory sequences have not been completely defined, DNA fragments of different lengths may have identical promoter activity.

The “3′ non-coding sequences” refer to DNA sequences located downstream of a coding sequence and include polyadenylation recognition sequences and other sequences encoding regulatory signals capable of affecting mRNA processing or gene expression. The polyadenylation signal is usually characterized by affecting the addition of polyadenylic acid tracts to the 3′ end of the mRNA precursor. The use of different 3′ non-coding sequences is exemplified by Ingelbrecht et al. (Plant Cell 1:671-680 (1989)).

“RNA transcript” refers to the product resulting from RNA polymerase-catalyzed transcription of a DNA sequence. When the RNA transcript is a perfect complementary copy of the DNA sequence, it is referred to as the primary transcript or it may be a RNA sequence derived from post-transcriptional processing of the primary transcript and is referred to as the mature RNA. “Messenger RNA (mRNA)” refers to the RNA that is without introns and that can be translated into protein by the cell. “cDNA” refers to a double-stranded DNA that is complementary to and derived from mRNA. “Sense” RNA refers to RNA transcript that includes the mRNA and so can be translated into protein by the cell. “Antisense RNA” refers to a RNA transcript that is complementary to all or part of a target primary transcript or mRNA and that blocks the expression of a target gene (U.S. Pat. No. 5,107,065; WO 9928508). The complementarity of an antisense RNA may be with any part of the specific gene transcript, i.e., at the 5′ non-coding sequence, 3′ non-coding sequence, or the coding sequence. “Functional RNA” refers to antisense RNA, ribozyme RNA, or other RNA that is not translated yet has an effect on cellular processes.

The term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence (i.e., that the coding sequence is under the transcriptional control of the promoter). Coding sequences can be operably linked to regulatory sequences in sense or antisense orientation.

The term “expression”, as used herein, refers to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from the nucleic acid fragment of the invention. Expression may also refer to. translation of mRNA into a polypeptide. “Antisense inhibition” refers to the production of antisense RNA transcripts capable of suppressing the expression of the target protein. “Overexpression” refers to the production of a gene product in transgenic organisms that exceeds levels of production in normal or non-transformed organisms. “Co-suppression” refers to the production of sense RNA transcripts capable of suppressing the expression of identical or substantially similar foreign or endogenous genes (U.S. Pat. No. 5,231,020).

The term “altered biological activity” will refer to an activity, associated with a protein encoded by a microbial nucleotide sequence which can be measured by an assay method, where that activity is either greater than or less than the activity associated with the native microbial sequence. “Enhanced biological activity” refers to an altered activity that is greater than that associated with the native sequence. “Diminished biological activity” is an altered activity that is less than that associated with the native sequence.

“Mature” protein refers to a post-translationally processed polypeptide; i.e., one from which any pre- or propeptides present in the primary translation product have been removed. “Precursor” protein refers to the primary product of translation of mRNA; i.e., with pre- and propeptides still present. Pre- and propeptides may be but are not limited to intracellular localization signals.

A “chloroplast transit peptide” is an amino acid sequence which is translated in conjunction with a protein and directs the protein to the chloroplast or other plastid types present in the cell in which the protein is made. “Chloroplast transit sequence” refers to a nucleotide sequence that encodes a chloroplast transit peptide.

“Transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism, resulting in genetically stable inheritance. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.

The terms “plasmid”, “vector” and “cassette” refer to an extra chromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA fragments. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell. “Transformation cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that facilitate transformation of a particular host cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.

The term “sequence analysis software” refers to any computer algorithm or software program that is useful for the analysis of nucleotide or amino acid sequences. “Sequence analysis software” may be commercially available or independently developed. Typical sequence analysis software will include but is not limited to the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wis.), BLAST P, BLASTN, BLASTX (Altschul et al., J. Mol. Biol. 215:403-410 (1990), Vector NTI (InforMax Inc., North Bethesda, Md.) and DNASTAR (DNASTAR Inc., Madison, Wis.). Within the context of this application it will be understood that where sequence analysis software is used for analysis, that the results of the analysis will be based on the “default values” of the program referenced, unless otherwise specified. As used herein “default vales” will mean any set of values or parameters which originally load with the software when first initialized.

The term “conserved domain” means a set of amino acids conserved at specific positions along an aligned sequence of evolutionarily related proteins. While amino acids at other positions can vary between homologous proteins, amino acids that are highly conserved at specific positions indicate amino acids that are essential in the structure, the stability, or the activity of a protein. Because they are identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers, or “signatures”, to determine if a protein with a newly determined sequence belongs to a previously identified protein family. Conserved domains of are specifically described for the family of cis-prenyltransferases, according to the work of Apfel, C. M. et al. (J. Bact. 181(2): 483-492 (1999)).

The term “non-conserved domain” means a set of amino acids, present between conserved domains, which whilst the individual amino acids are not conserved at specific positions along an aligned sequence of evolutionarily related proteins, is recognizable by its presence or absence in aligned sequences of evolutionary related proteins. The presence of such a domain, despite positional non-conservation among its constituent amino acids, indicates that the domain plays a role essential in the structure, the stability, or the activity of a protein, e.g., by increasing the distance between other (conserved) domains. Because they are identified by their presence in aligned sequences of a family of protein homologues, they can be used as identifiers, or “signatures”, to determine if a protein with a newly determined sequence belongs to a previously identified protein family or subfamily. In the present invention, non-conserved domains are specifically described for cis-prenyltransferases from rubber-producing plants.

Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by: Sambrook, J., Fritsch, E. F. and Maniatis, T., Molecular Cloning: A Laboratory Manual; 2nd ed.; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1989 (hereinafter “Maniatis”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions; Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1984; and by Ausubel, F. M. et al., Current Protocols in Molecular Biology; Greene Publishing Assoc. and Wiley-Interscience (1987).

Cis-Prenyltransferase Sequence Identification

Novel nucleotide sequences have been isolated from the rubber-producing plants Taraxacum kok-saghyz (russian dandelion) and Helianthus annus (sunflower) encoding gene products involved in the production of natural rubbers. More specifically, these unique plant homologs of microbial cis-prenyltransferase proteins are involved in the synthesis of poly cis-isoprenoids. Classification of the proteins is based on alignments which reveal the presence of five conserved domains, indicative of a cis-prenyltransferase, as described by Apfel et al. (J. Bact. 181(2): 483-492 (1999)).

Comparison of the dandelion cis-prenyltransferase nucleotide base and deduced amino acid sequences to public databases reveals that the most similar known sequences are about 50% identical to the amino acid sequence of SEQ ID NO:4 reported herein over a length of 301 amino acids using a Smith-Waterman alignment algorithm (W. R. Pearson, Comput. Methods Genome Res., [Proc. Int. Symp.] (1994), Meeting Date 1992,111-20. Suhai, S., Ed.; Plenum: New York, N.Y.). Strong correlation was seen between the instant sequences and the cis-prenyltransferase genes and proteins isolated from Micrococcus luteus (SEQ ID NOs:17 and 18, encoding undecaprenyl diphosphate synthase; Shimizu, N., et al., J. Biol. Chem. 273:19476-19481 (1998)) and Saccharomyces cerevisiae (SEQ ID NOs: 19-22).

In like manner, comparison of the sunflower cis-prenyltransferase nucleotide base and deduced amino acid sequences to public databases reveals that the most similar known sequences are about 57% identical to the amino acid sequence of SEQ ID NO: 6 reported herein over a length of 168 amino acids using a Smith-Waterman alignment algorithm. Again, strong correlation was noted between the instant sequences and the cis-prenyltransferase genes and proteins isolated from Micrococcus luteus (SEQ ID NOs:17 and 18; Shimizu, N., et al., supra) and Saccharomyces cerevisiae (SEQ ID NOs:19-22).

More preferred cis-prenyltransferase amino acid fragments are at least about 70%-80% identical to the sequences herein, where about 80%-90% is preferred. Most preferred are nucleic acid fragments that are at least 95% identical to the amino acid fragments reported herein.

Similarly, preferred cis-prenyltransferase encoding nucleic acid sequences corresponding to the instant ORF's are those encoding active proteins and which are at least 80% identical to the nucleic acid sequences of reported herein. More preferred cis-prenyltransferase nucleic acid fragments are at least 90% identical to the sequences herein. Most preferred are cis-prenyltransferase nucleic acid fragments that are at least 95% identical to the nucleic acid fragments reported herein.

Isolation of Homologs

The nucleic acid fragments of the present invention may be used to isolate cDNAs and genes encoding homologous prenyltransferases from the same or other plant species or from microbial species. Isolating homologous genes using sequence-dependent protocols is well known in the art. Examples of sequence-dependent protocols include (but are not limited to) methods of nucleic acid hybridization and methods of DNA and RNA amplification, as exemplified by various uses of nucleic acid amplification technologies (e.g. polymerase chain reaction (PCR), Mullis et al., U.S. Pat. No. 4,683,202; ligase chain reaction (LCR), Tabor, S. et al., Proc. Acad. Sci, USA 82:1074, (1985); or strand displacement amplification (SDA), Walker, et al., Proc. Natl. Acad. Sci. U.S.A., 89: 392 (1992)).

For example, other cis-prenyltransferase genes sharing significant homology to those of the instant invention, either as cDNAs or genomic DNAs, could be isolated directly by using all or a portion of the instant nucleic acid fragments as DNA hybridization probes to screen libraries from any desired plant using methodology well known to those skilled in the art. Specific oligonucleotide probes based upon the instant nucleic acid sequences can be designed and synthesized by methods known in the art (Maniatus, supra). Moreover, the entire sequences can be used directly to synthesize DNA probes by methods known to the skilled artisan such as random primers, DNA labeling, nick translation, or end-labeling techniques, or RNA probes using available in vitro transcription systems. In addition, specific primers can be designed and used to amplify a part of (or full-length of) the present sequence. The resulting amplification products can be labeled directly during amplification reactions or labeled after amplification reactions, and used as probes to isolate full length DNA fragments under conditions of appropriate stringency.

Typically, in PCR-type amplification techniques, the primers have different sequences and are not complementary to each other. Depending on the desired test conditions, the sequences of the primers should be designed to provide for both efficient and faithful replication of the target nucleic acid. Methods of PCR primer design are common and well known in the art. (Thein and Wallace, “The use of oligonucleotide as specific hybridization probes in the Diagnosis of Genetic Disorders”, in Human Genetic Diseases: A Practical Approach; K. E. Davis, Ed.; IRL: Herndon, Va., 1986; pp 33-50); Rychlik, W., In Methods in Molecular Biology; PCR Protocols: Current Methods and Applications. White, B. A., Ed.; Humania: Totowa, N.J., 1993; Vol. 15, pp 31-39).

Generally two short segments of the instant sequences may be used in polymerase chain reaction protocols to amplify longer nucleic acid fragments encoding homologous genes from DNA or RNA. The polymerase chain reaction may also be performed on a library of cloned nucleic acid fragments wherein the sequence of one primer is derived from the instant nucleic acid fragments, and the sequence of the other primer takes advantage of the presence of the polyadenylic acid tracts to the 3′ end of the mRNA precursor encoding plant UPPS homologs.

Alternatively, the second primer sequence may be based upon sequences derived from the cloning vector. For example, the skilled artisan can follow the RACE protocol (Frohman et al., Proc. Natl. Acad. Sci. USA 85:8998 (1988)) to generate cDNAs by using PCR to amplify copies of the region between a single point in the transcript and the 3′ or 5′ end. Primers oriented in the 3′ and 5′ directions can be designed from the instant sequences. Using commercially available 3′ RACE or 5′ RACE systems (BRL), specific 3′ or 5′ cDNA fragments can be isolated (Ohara et al., Proc. Natl. Acad. Sci., USA 86:5673 (1989); Loh et al., Science 243:217 (1989)). Products generated by the 3′ and 5′ RACE procedures can be combined to generate full-length cDNAs (Frohman et al., Techniques 1:165 (1989)).

Alternatively the instant sequences may be employed as hybridization reagents for the identification of homologs. The basic components of a nucleic acid hybridization test include a probe, a sample suspected of containing the gene or gene fragment of interest, and a specific hybridization method. Probes of the present invention are typically single stranded nucleic acid sequences that are complementary to the nucleic acid sequences to be detected. Probes are “hybridizable” to the nucleic acid sequence to be detected. The probe length can vary from 5 bases to tens of thousands of bases, and will depend upon the specific test to be done. Typically a probe length of about 15 bases to about 30 bases is suitable. Only part of the probe molecule need be complementary to the nucleic acid sequence to be detected. In addition, the complementarity between the probe and the target sequence need not be perfect. Hybridization does occur between imperfectly complementary molecules with the result that a certain fraction of the bases in the hybridized region are not paired with the proper complementary base.

Hybridization methods are well defined. Typically the probe and sample must be mixed under conditions which will permit nucleic acid hybridization. This involves contacting the probe and sample in the presence of an inorganic or organic salt under the proper concentration and temperature conditions. The probe and sample nucleic acids must be in contact for a long enough time that any possible hybridization between the probe and sample nucleic acid may occur. The concentration of probe or target in the mixture will determine the time necessary for hybridization to occur. The higher the probe or target concentration the shorter the hybridization incubation time needed. Optionally a chaotropic agent may be added. The chaotropic agent stabilizes nucleic acids by inhibiting nuclease activity. Furthermore, the chaotropic agent allows sensitive and stringent hybridization of short oligonucleotide probes at room temperature (Van Ness and Chen, Nucl. Acids Res., 19:5143-5151 (1991)). Suitable chaotropic agents include guanidinium chloride, guanidinium thiocyanate, sodium thiocyanate, lithium tetrachloroacetate, sodium perchlorate, rubidium tetrachloroacetate, potassium iodide, and cesium trifluoroacetate, among others. Typically, the chaotropic agent will be present at a final concentration of about 3M. If desired, one can add formamide to the hybridization mixture, typically 30-50% (v/v).

Various hybridization solutions can be employed. Typically, these comprise from about 20 to 60% volume, preferably 30%, of a polar organic solvent. A common hybridization solution employs about 30-50% v/v formamide, about 0.15 to 1M sodium chloride, about 0.05 to 0.1M buffers, such as sodium citrate, Tris-HCl, PIPES or HEPES (pH range about 6-9), about 0.05 to. 0.2% detergent, such as sodium dodecylsulfate, or between 0.5-20 mM EDTA, FICOLL (Pharmacia Inc.) (about 300-500 kilodaltons), polyvinylpyrrolidone (about 250-500 kdal), and serum albumin. Also included in the typical hybridization solution will be unlabeled carrier nucleic acids from about 0.1 to 5 mg/mL, fragmented nucleic DNA, e.g., calf thymus or salmon sperm DNA, or yeast RNA, and optionally from about 0.5 to 2% wt/vol glycine. Other additives may also be included, such as volume exclusion agents which include a variety of polar water-soluble or swellable agents, such as polyethylene glycol, anionic polymers such as polyacrylate or polymethylacrylate, and anionic saccharidic polymers, such as dextran sulfate.

Nucleic acid hybridization is adaptable to a variety of assay formats. One of the most suitable is the sandwich assay format. The sandwich assay is particularly adaptable to hybridization under non-denaturing conditions. A primary component of a sandwich-type assay is a solid support. The solid support has adsorbed to it or covalently coupled to it immobilized nucleic acid probe that is unlabeled and complementary to one portion of the sequence.

Finally, availability of the instant nucleotide and deduced amino acid sequences facilitates immunological screening of DNA expression libraries. Synthetic peptides representing portions of the instant amino acid sequence may be synthesized. These peptides can be used to immunize animals to produce polyclonal or monoclonal antibodies with specificity for peptides or proteins comprising the amino acid sequences. These antibodies can be then be used to screen DNA expression libraries to isolate full-length DNA clones of interest (Lerner et al., Adv. Immunol. 36:1 (1984); Maniatus, supra).

Recombinant Expression—Plants

It is expected that introduction of chimeric genes encoding the instant cis-prenyltransferase enzymes, under the control of the appropriate promoters, will enable increased production of natural rubbers when an appropriate source of IPP is present in the cell to produce appropriate initiator molecules (DMAPP, GPP, FPP or GGPP). It is contemplated that it will be useful to express the instant genes both in natural host cells as well as heterologous plant hosts.

The nucleic acid fragments of the instant invention may also be used to create transgenic plants in which any of the instant cis-prenyltransferase proteins are present at higher or lower levels than normal, thus permitting modification to the production of natural rubbers. Introduction of the nucleic acid fragments of the instant invention into transgenic plants may have benefit in modifying the rate or timing of rubber production, the amount and/or quality of the rubber produced, and/or the allergenic properties of the resultant rubber. Alternatively, in some applications, it might be desirable to express any of the instant cis-prenyltransferases in specific plant tissues and/or cell types, or during developmental stages in which they would normally not be encountered. The expression of full-length plant cis-prenyltransferase cDNAs yields a mature protein capable of the synthesis of cis-polyisoprenoids from IPP as the substrate. The presence of an initiator allylic isoprenoid diphosphate enhances this activity.

Further, it is contemplated that transgenic plants expressing any of the instant cis-prenyltransferase sequences will have altered or modulated defense mechanisms against various pathogens and natural predators. For example, various latex proteins are known to be antigenic and recognized by IgE antibodies, suggesting their role in immunolgical defense (Yagami et al., Journal of Allergy and Clinical Immunology, 101(3): 379-385 (1998)). Additionally it has been shown that a significant portion of the latex isolated from Hevea brasiliensis contains chitinases/lysozymes, which are capable of degrading the chitin component of fungal cell walls and the peptidoglycan component of bacterial cell walls (Martin, M. N., Plant Physiol (Bethesda), 95 (2): 469-476 (1991)). It is therefore an object of the instant invention to provide transgenic plants having altered, modulated or increased defenses towards various pathogens and herbivores.

Preferred Plant Hosts and Transformation Methods

Preferred plant hosts will be any variety that will support a high production level of the instant cis-prenyltransferase sequences. Suitable plant species include those plant species which produce natural rubber (e.g., Hevea brasiliensis, Taraxacum spp.), but are not limited to: tobacco (Nicotiana spp.), tomato (Lycopersicon spp.), potato (Solanum spp.), hemp (Cannabis spp.), sunflower (Helianthus spp.), sorghum (Sorghum vulgare), wheat (Triticum spp.), maize (Zea mays), rice (Oryza sativa), rye (Secale cereale), oats (Avena spp.), barley (Hordeum vulgare), rapeseed (Brassica spp.), broad bean (Vicia faba), french bean (Phaseolus vulgaris), other bean species (Vigna spp.), lentil (Lens culinaris), soybean (Glycine max), arabidopsis (Arabidopsis thaliana), guayule (Parthenium argentatum), cotton (Gossypium hirsutum), petunia (Petunia hybrida), flax (Linum usitatissimum), and carrot (Daucus carota sativa).

One skilled in the art recognizes that the expression level and regulation of a transgene in a plant can vary significantly from line to line. Thus, one has to test several lines to find one with the desired expression level and regulation.

A variety of techniques are available and known to those skilled in the art for introduction of constructs into a plant cell host. These techniques include transformation with DNA employing A. tumefaciens or A. rhizogenes as the transforming agent, electroporation, particle acceleration, etc. (see, for example, EP 295959 and EP 138341). It is particularly preferred to use the binary type vectors of Ti and Ri plasmids of Agrobacterium spp. Ti-derived vectors transform a wide variety of higher plants, including monocotyledonous and dicotyledonous plants, such as soybean, cotton, rape, tobacco, and rice (Pacciofti et al., Bio/Technology 3:241 (1985); Byme et al., Plant Cell, Tissue and Organ Culture 8:3 (1987); Sukhapinda et al., Plant Mol. Biol. 8:209-216 (1987); Lorz et al., Mol. Gen. Genet. 199:178 (1985); Potrykus, Mol. Gen. Genet. 199:183 (1985); Park et al., J. Plant Biol. 38(4):365-71 (1995); Hiei et al., Plant J. 6:271-282 (1994)). The use of T-DNA to transform plant cells has received extensive study and is amply described (EP 120516; Hoekema, In: The Binary Plant Vector System, Offset-drukkerij Kanters B. V.; Alblasserdam (1985), Chapter V; Knauf, et al., Genetic Analysis of Host Range Expression by Agrobacterium, In: Molecular Genetics of the Bacteria-Plant Interaction, Puhler, A. Ed.; Springer-Verlag: N.Y., 1983, p 245; and An, et al., EMBO J. 4:277-284 (1985)). For introduction into plants, the chimeric genes of the invention can be inserted into binary vectors as described in the examples.

Other transformation methods are available to those skilled in the art, such as direct uptake of foreign DNA constructs (see EP 295959), techniques of electroporation (see Fromm et al., Nature (London) 319:791 (1986)) or high-velocity ballistic bombardment with metal particles coated with the nucleic acid constructs (see Kline et al., Nature (London) 327:70 (1987), and see U.S. Pat. No. 4,945,050). Once transformed, the cells can be regenerated by those skilled in the art. Of particular relevance are the recently described methods to transform foreign genes into commercially important crops, such as rapeseed (see De Block et al., Plant Physiol. 91:694-701 (1989)), sunflower (Everett et al., Bio/Technology 5:1201 (1987)), soybean (McCabe et al., Bio/Technology 6:923 (1988); Hinchee et al., Bio/Technology 6:915 (1988); Chee et al., Plant Physiol. 91:1212-1218 (1989); Christou et al., Proc. Natl. Acad. Sci USA 86:7500-7504 (1989); EP 301749), rice (Hiei et al., Plant J. 6:271-282 (1994)), corn (Gordon-Kamm et al., Plant Cell 2:603-618 (1990); Fromm et al., Biotechnology 8:833-839 (1990)), and Hevea (Yeang, H. Y., et al., Rubber Latex as an Expression System for High-value Proteins. In, Engineering Crop Plants for Industrial End Uses. Shewry, P. R., Napier, J. A., David, P. J., Eds.; Portland: London, 1998; pp 55-64).

Transgenic plant cells are then placed in an appropriate selective medium for selection of transgenic cells that are then grown to callus. Shoots are grown from callus and plantlets generated from the shoot by growing in rooting medium. The various constructs normally will be joined to a marker for selection in plant cells. Conveniently, the marker may be resistance to a biocide (particularly an antibiotic such as kanamycin, G418, bleomycin, hygromycin, chloramphenicol, herbicide, or the like). The particular marker used will allow for selection of transformed cells as compared to cells lacking the DNA that has been introduced. Components of DNA constructs including transcription cassettes of this invention may be prepared from sequences which are native (endogenous) or foreign (exogenous) to the host. By “foreign” it is meant that the sequence is not found in the wild-type host into which the construct is introduced. Heterologous constructs will contain at least one region that is not native to the gene from which the transcription-initiation-region is derived.

To confirm the presence of the transgenes in transgenic cells and plants, a Southern blot analysis can be performed using methods known to those skilled in the art. Expression products of the transgenes can be detected in any of a variety of ways, depending upon the nature of the product, and include Western blot and enzyme assay. One particularly useful way to quantitate protein expression and to detect replication in different plant tissues is to use a reporter gene, such as GUS. Once transgenic plants have been obtained, they may be grown to produce plant tissues or parts having the desired phenotype. The plant tissue or plant parts may be harvested, and/or the seed collected. The seed may serve as a source for growing additional plants with tissues or parts having the desired characteristics.

Construction of Chimeric Genes for Transformation

Overexpression of the instant cis-prenyltransferases may be accomplished by first constructing chimeric genes in which the coding region is operably-linked to promoters capable of directing expression of a gene in the desired tissues at the desired stage of development. For reasons of convenience, the chimeric genes may comprise promoter sequences and translation leader sequences derived from the same genes. 3′ Non-coding sequences encoding transcription termination signals must also be provided. The instant chimeric gene may also comprise one or more introns in order to facilitate gene expression.

Any combination of any promoter and any terminator capable of inducing expression of a coding region may be used in the chimeric genetic sequence. Some suitable examples of promoters and terminators include those from nopaline synthase (nos), octopine synthase (ocs) and cauliflower mosaic virus (CaMV) genes. One type of efficient plant promoter that may be used is a high-level plant promoter. Such promoters, in operable linkage with the genetic sequences or the present invention should be capable of promoting expression of the present gene product. High level plant promoters that may be used in this invention, for example, include the promoter of the small subunit (ss) of the ribulose-1,5-bisphosphate carboxylase from soybean (Berry-Lowe et al., J. Molecular and App. Gen., 1:483-498 (1982)), and the promoter of the chlorophyll a/b binding protein. These two promoters are known to be light-induced in plant cells (see, for example, Genetic Engineering of Plants, an Agricultural Perspective, A. Cashmore, Ed.; Plenum: NY, 1983; pp 29-38; Coruzzi, G. et al., The Journal of Biological Chemistry, 258:1399 (1983); and Dunsmuir, P. et al., Journal of Molecular and Applied Genetics, 2:285 (1983)).

Plasmid vectors comprising the instant chimeric genes can then be constructed. The choice of a plasmid vector depends upon the method that will be used to transform host plants. The skilled artisan is well aware of the genetic elements that must be present on the plasmid vector in order to successfully transform, select and propagate host cells containing the chimeric gene. The skilled artisan will also recognize that different independent transformation events will result in different levels and patterns of expression (Jones et al., EMBO J. 4:2411-2418 (1985); De Almeida et al., Mol. Gen. Genetics 218:78-86 (1989)), and thus that multiple events must be screened in order to obtain lines displaying the desired expression level and pattern. Such screening may be accomplished by Southern analysis of DNA blots (Southern, J. Mol. Biol. 98: 503 (1975)), Northern analysis of mRNA expression (Kroczek, J. Chromatogr. Biomed. Appl., 618(1-2): 133-145 (1993)), Western analysis of protein expression, or phenotypic analysis.

For some applications it may be useful to direct the cis-prenyltransferase proteins to different cellular compartments or to facilitate their secretion from the cell. It is thus envisioned that the chimeric genes described above may be further modified by the addition of appropriate intracellular or extracellular targeting sequences to their coding regions (and/or with targeting sequences that are already present removed). These additional targeting sequences include chloroplast transit peptides (Keegstra et al., Cell 56:247-253 (1989)), signal sequences that direct proteins to the endoplasmic reticulum (Chrispeels et al., Ann. Rev. Plant Phys. Plant Mol. 42:21-53 (1991)), and nuclear localization signal (Raikhel et al., Plant Phys. 100:1627-1632 (1992)). While the references cited give examples of each of these, the list is not exhaustive and more targeting signals of utility may be discovered in the future which are useful in the invention.

Recombinant Expression—Microbial

The genes and gene products of the instant sequences may also be produced in heterologous host cells, particularly in the cells of microbial hosts. Production of natural rubbers in microbial hosts will be useful when an appropriate source of IPP is present in the cell to produce appropriate initiator molecules (DMAPP, GPP, FPP or GGPP). Expression in recombinant microbial hosts may be useful for the expression of various pathway intermediates; or for the modulation of pathways already existing in the host for the synthesis of new products heretofore not possible using the host. Additionally, recombinant expression may be useful for the preparation of antibodies to the cis-prenyltransferase protein by-methods well known to those skilled in the art. The antibodies would be useful for detecting the instant cis-prenyltransferase proteins in situ in cells or in vitro in cell extracts.

Preferred Microbial Hosts and Transformation Methods

Preferred heterologous host cells for expression of the instant genes and nucleic acid fragments are microbial hosts that can be found broadly within the fungal or bacterial families and which grow over a wide range of temperature, pH values, and solvent tolerances. For example, it is contemplated that any bacteria, yeast, and filamentous fungi will be suitable hosts for expression of the present nucleic acid fragments. Because transcription, translation and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, functional genes are expressed irrespective of carbon feedstock used to generate cellular biomass. Large-scale microbial growth and functional gene expression may utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, or saturated hydrocarbons such as methane or carbon dioxide (in the case of photosynthetic or chemoautotrophic hosts). However, the functional genes may be regulated, repressed or depressed by specific growth conditions, which may include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions. In addition, the regulation of functional genes may be achieved by the presence or absence of specific regulatory molecules that are added to the culture and are not typically considered nutrient or energy sources. Growth rate may also be an important regulatory factor in gene expression. Examples of host strains include but are not limited to bacterial (e.g., Bacillus, Escherichia, Salmonella and Shigella), fungal, or yeast species (e.g., Aspergillus, Saccharomyces, Pichia, Candida and Hansenula).

Methods for the transformation of such hosts and the expression of foreign proteins are well known in the art and examples of suitable protocols may be found In Manual of Methods for General Bacteriology; Gerhardt et al., Eds.; American Society for Microbiology: Washington, D.C., 1994 or In Biotechnology: A Textbook of Industrial Microbiology, 2^(nd) ed., Brock, T. D., Ed.; Sinauer Associates: Sunderland, Mass., 1989.

Construction of Chimeric Genes for Transformation

Microbial expression systems and expression vectors containing regulatory sequences that direct high level expression of foreign proteins are well known to those skilled in the art. Any of these could be used to construct chimeric genes for production of the instant cis-prenyltransferases. These chimeric genes could then be introduced into appropriate microorganisms via transformation to provide high level expression of the instant cis-prenyltransferase proteins.

Vectors or cassettes useful for the transformation of suitable microbial host cells are well known in the art. Typically the vector or cassette contains sequences directing transcription and translation of the relevant gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. Suitable vectors comprise a region 5′ of the gene that harbors transcriptional initiation controls and a region 3′ of the DNA fragment that controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.

Initiation control regions or promoters that are useful to drive expression of the instant cis-prenyltransferases in the desired microbial host cell are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these genes is suitable for the instant invention including, but not limited to: CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, ara, tet, trp, IP_(L), IP_(R), T7, tac, and trc (useful for expression in Escherichia coli) as well as the amy, apr, npr promoters and various phage promoters (useful for expression in Bacillus).

Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.

Industrial Production in Microbial Hosts

Where commercial production of the instant enzymes are desired a variety of culture methodologies may be applied. For example, large-scale production of a specific gene product overexpressed from a recombinant microbial host may be produced by both batch or continuous culture methodologies.

A classical batch culturing method is a closed system where the composition of the media is set at the beginning of the culture and not subject to artificial alterations during the culturing process. Thus, at the beginning of the culturing process the media is inoculated with the desired organism or organisms and growth or metabolic activity is permitted to occur adding nothing to the system. Typically, however, a “batch” culture is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the culture is terminated. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase are often responsible for the bulk of production of end product or intermediate in some systems. Stationary or post-exponential phase production can be obtained in other systems.

A variation on the standard batch system is the Fed-Batch system. Fed-Batch culture processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the culture progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO₂. Batch and Fed-Batch culturing methods are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2^(nd) ed., Brock, T. D., Ed.; Sinauer Associates: Sunderland, Mass., 1989; or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36: 227 (1992), herein incorporated by reference.

Commercial production of the instant cis-prenyltransferases and their proteins may also be accomplished with a continuous culture. Continuous cultures are open systems where a defined culture media is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing. Continuous cultures generally maintain the cells at a constant high liquid phase density where cells are primarily in log phase growth. Alternatively, continuous culture may be practiced with immobilized cells where carbon and nutrients are continuously added and valuable products, by-products, or waste products are continuously removed from the cell mass. Cell immobilization may be performed using a wide range of solid supports composed of natural and/or synthetic materials.

Continuous or semi-continuous culture allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to media being drawn off must be balanced against the cell growth rate in the culture. Methods of modulating nutrients and growth factors for continuous culture processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.

Fermentation media in the present invention must contain suitable carbon substrates. Suitable substrates may include, but are not limited to: monosaccharides (e.g., glucose and fructose), oligosaccharides (e.g., lactose or sucrose), polysaccharides (e.g., starch, cellulose, or mixtures thereof), and unpurified mixtures from renewable feedstocks (e.g., cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt). Additionally the carbon substrate may also be one-carbon substrates such as carbon dioxide, methane or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates, methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1 Compd., [Int. Symp.], 7^(th) ed.; Murrell, J. Collin; Kelly, Don P., Eds.; Intercept: Andover, UK, 1993; pp 415-32). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol. 153:485-489 (1990)). Hence it is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of host organism.

Pathway Engineering

Knowledge of the sequence of the present genes will be useful in manipulating the polyisoprenoid biosynthetic pathways in any organism having such a pathway and particularly in other rubber producing plants. Methods of manipulating genetic pathways are common and well known in the art. Selected genes in a particularly pathway may be up-regulated or down-regulated by variety of methods. Additionally, competing pathways in an organism may be eliminated or sublimated by gene disruption and similar techniques.

Once a key genetic pathway has been identified and sequenced, specific genes may be up-regulated to increase the output of the pathway. For example, additional copies of the targeted genes may be introduced into the host cell on multicopy plasmids such as pBR322. Alternatively the target genes may be modified so as to be under the control of non-native promoters. Where it is desired that a pathway operate at a particular point in a cell cycle or during a fermentation run, regulated or inducible promoters may used to replace the native promoter of the target gene. Similarly, in some cases the native or endogenous promoter may be modified to increase gene expression. For example, endogenous promoters can be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, U.S. Pat. No. 5,565,350; Zarling et al., PCT/US93/03868).

Alternatively, it may be necessary to reduce or eliminate the expression of certain genes in the target pathway or in competing pathways that may serve as competing sinks for energy or carbon. Methods of down-regulating genes for this purpose have been explored.

For example, where sequence of the gene to be disrupted is known, one of the most effective methods for gene down-regulation is targeted gene disruption where foreign DNA is inserted into a structural gene so as to disrupt transcription. This can be effected by the creation of genetic cassettes comprising the DNA to be inserted (often a genetic marker) flanked by sequences having a high degree of homology to a portion of the gene to be disrupted. Introduction of the cassette into the host cell results in insertion of the foreign DNA into the structural gene via the native DNA replication mechanisms of the cell (see for example Hamilton et al. J. Bacteiol. 171:4617-4622 (1989); Balbas et al. Gene 136:211-213 (1993); Gueldener et al. Nucleic Acids Res. 24:2519-2524 (1996); and Smith et al. Methods Mol. Cell. Biol. 5:270-277(1996)).

Alternative methods are available to reduce or eliminate expression of genes encoding the instant polypeptides, if desirable in plants for some applications. In order to accomplish this, a chimeric gene designed for co-suppression of the instant polypeptide can be constructed by linking a gene or gene fragment encoding that polypeptide to plant promoter sequences. Antisense technology requires that a nucleic acid segment from the desired gene is cloned and operably linked to a promoter such that the anti-sense strand of RNA will be transcribed. This construct is then introduced into the host cell and the antisense strand of RNA is produced. Antisense RNA inhibits gene expression by preventing the accumulation of mRNA which encodes the protein of interest. The person skilled in the art will know that special considerations are associated with the use of antisense technologies in order to reduce expression of particular genes. For example, the proper level of expression of antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. Nonetheless, either the co-suppression or antisense chimeric genes could be introduced into plants via transformation wherein expression of the corresponding endogenous genes is reduced or eliminated.

Finally, one recent variation upon “classical” antisense and cosuppression methodologies is embodied in WO 02/00904, published on Jan. 3, 2002. Specifically, it was found that suitable nucleic acid sequences and their reverse complement can be used to alter the expression of any mRNA encoding a protein of interest which is in proximity to the suitable nucleic acid sequence and its reverse complement. Surprisingly, the suitable nucleic acid sequence and its reverse complement can be either unrelated to any endogenous RNA in the host or can be encoded by any nucleic acid sequence in the genome of the host provided that the nucleic acid sequence does not encode any target mRNA or any sequence that is substantially similar to the target mRNA. A preferred artificial and non-naturally occurring, sequence is that encoded by the peptide “ELVISLIVES” (SEQ ID NO:35). This approach permits a very efficient and robust approach to achieving single, or multiple, gene co-suppression using single plasmid transformation.

Molecular genetic solutions to the generation of plants with altered gene expression have a decided advantage over more traditional plant breeding approaches. Changes in plant phenotypes can be produced by specifically inhibiting expression of one or more genes by antisense inhibition or cosuppression or similar methodologies thereto (U.S. Pat. No. 5,190,931; U.S. Pat. No. 5,107,065; U.S. Pat. No. 5,283,323; WO 02/00904). An antisense or cosuppression construct would act as a dominant negative regulator of gene activity. While conventional mutations can yield negative regulation of gene activity, these effects are most likely recessive. The dominant negative regulation available with a transgenic approach may be advantageous from a breeding perspective. In addition, the ability to restrict the expression of specific phenotype to the reproductive tissues of the plant by the use of tissue specific promoters may confer agronomic advantages relative to conventional mutations that may have an effect in all tissues in which a mutant gene is ordinarily expressed.

A person skilled in the art will know that special considerations are associated with the use of antisense or cosuppression technologies in order to reduce expression of particular genes. For example, the proper level of expression of sense or antisense genes may require the use of different chimeric genes utilizing different regulatory elements known to the skilled artisan. Once transgenic plants are obtained by one of the methods described above, it will be necessary to screen individual transgenics for those that most effectively display the desired phenotype. Accordingly, the skilled artisan will develop methods for screening large numbers of transformants. The nature of these screens will generally be chosen on practical grounds, and is not an inherent part of the invention. For example, one can screen by looking for changes in gene expression by using antibodies specific for the protein encoded by the gene being suppressed, or one could establish assays that specifically measure enzyme activity. A preferred method will be one that allows large numbers of samples to be processed rapidly, since it will be expected that a large number of transformants will be negative for the desired phenotype.

Although targeted gene disruption and antisense technology offer effective means of down-regulating genes where the sequence is known, other less specific methodologies have been developed that are not sequence based. For example, cells may be exposed to UV radiation and then screened for the desired phenotype. Mutagenesis with chemical agents is also effective for generating mutants and commonly used substances include chemicals that affect nonreplicating DNA such as HNO₂ and NH₂OH, as well as agents that affect replicating DNA such as acridine dyes, notable for causing frameshift mutations. Specific methods for creating mutants using radiation or chemical agents are well documented in the art. See, for example: Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, 2^(nd) ed., Brock, T. D., Ed.; Sinauer Associates: Sunderland, Mass., 1989; or Deshpande, Mukund V., Appl. Biochem. Biotechnol., 36: 227 (1992).

Another non-specific method of gene disruption is the use of transposable elements or transposons. Transposons are genetic elements that insert randomly in DNA but can be later retrieved on the basis of sequence to determine where the insertion has occurred. Both in vivo and in vitro transposition methods are known. Both methods involve the use of a transposable element in combination with a transposase enzyme. When the transposable element or transposon is contacted with a nucleic acid fragment in the presence of the transposase, the transposable element will randomly insert into the nucleic acid fragment. The technique is useful for random mutagenesis and for gene isolation, since the disrupted gene may be identified on the basis of the sequence of the transposable element. Kits for in vitro transposition are commercially available (see for example The Primer Island Transposition Kit, available from Perkin Elmer Applied Biosystems, Branchburg, N.J., based upon the yeast Ty1 element; The Genome Priming System, available from New England Biolabs, Beverly, Mass., based upon the bacterial transposon Tn7; and the Ez::TN Transposon Insertion Systems, available from Epicentre Technologies, Madison, Wis., based upon the Tn5 bacterial transposable element).

Protein Engineering

It is contemplated that the instant nucleotides may be used to produce gene products having enhanced or altered activity. For example, the mutation of trans-prenyltransferases such as farnesyl diphosphate synthase to a form capable of generating a different and longer product (geranylgeranyl diphosphate) than the unmodified enzyme has been demonstrated (Ohnuma, S.-I. et al., J. Biol. Chem., 271(17): 10087-10095 (1996)). Various methods are known for mutating a native gene sequence to produce a gene product with altered or enhanced activity including, but not limited to:

-   -   1.) error prone PCR (Melnikov et al., Nucleic Acids Research,         27(4): 1056-1062 (Feb. 15, 1999));     -   2.) site directed mutagenesis (Coombs et al., Proteins;         Angeletti, Ruth Hogue, Ed.; Academic: San Diego, Calif., 1998;         pp 259-311, 1 plate); and     -   3.) “gene shuffling” (U.S. Pat. No. 5,605,793; U.S. Pat. No.         5,811,238; U.S. Pat. No. 5,830,721; and U.S. Pat. No. 5,837,458,         incorporated herein by reference).

The method of gene shuffling is particularly attractive due to its facile implementation, and high rate of mutagenesis and ease of screening. The process of gene shuffling involves the restriction endonuclease cleavage of a gene of interest into fragments of specific size in the presence of additional populations of DNA regions of both similarity to (or difference to) the gene of interest. This pool of fragments will then be denatured and reannealed to create a mutated gene. The mutated gene is then screened for altered activity.

The instant plant sequences of the present invention may be mutated and screened for altered or enhanced activity by this method. The sequences should be double stranded and can be of various lengths ranging from 50 bp to 10 kb. The sequences may be randomly digested into fragments ranging from about 10 bp to 1000 bp, using restriction endonucleases well known in the art (Maniatis, supra). In addition to the instant plant sequences, populations of fragments that are hybridizable to all or portions of the microbial sequence may be added. Similarly, a population of fragments that are not hybridizable to the instant sequence may also be added. Typically these additional fragment populations are added in about a 10 to 20 fold excess by weight as compared to the total nucleic acid. Generally, if this process is followed, the number of different specific nucleic acid fragments in the mixture will be about 100 to about 1000. The mixed population of random nucleic acid fragments are denatured to form single-stranded nucleic acid fragments and then reannealed. Only those single-stranded nucleic acid fragments having regions of homology with other single-stranded nucleic acid fragments will reanneal. The random nucleic acid fragments may be denatured by heating. One skilled in the art could determine the conditions necessary to completely denature the double stranded nucleic acid. Preferably the temperature is from about 80° C. to 100° C. The nucleic acid fragments may be reannealed by cooling. Preferably the temperature is from about 20° C. to 75° C. Renaturation can be accelerated by the addition of polyethylene glycol (“PEG”) or salt. A suitable salt concentration may range from 0 mM to 200 mM. The annealed nucleic acid fragments are then incubated in the presence of a nucleic acid polymerase and dNTPs (i.e., dATP, dCTP, dGTP and dTTP). The nucleic acid polymerase may be the Klenow fragment, the Taq polymerase or any other DNA. polymerase known in the art. The polymerase may be added to the random nucleic acid fragments prior to annealing, simultaneously with annealing or after annealing. The cycle of denaturation, renaturation and incubation in the presence of polymerase is repeated for a desired number of times. Preferably the cycle is repeated from 2 to 50 times, more preferably the sequence is repeated from 10 to 40 times. The resulting nucleic acid is a larger double-stranded polynucleotide ranging from about 50 bp to about 100 kb and may be screened for expression and altered activity by standard cloning and expression protocols (Manatis, supra).

Furthermore, a hybrid protein can be assembled by fusion of functional domains using the gene shuffling (exon shuffling) method (Nixon et al., PNAS, 94:1069-1073 (1997)). The functional domain of the instant gene can be combined with the functional domain of other genes to create novel enzymes with desired catalytic function. A hybrid enzyme may be constructed using PCR overlap extension methods and cloned into various expression vectors using the techniques well known to those skilled in art.

Other Applications

The instant cis-prenyltransferase proteins can be used as a target to facilitate the design and/or identification of inhibitors of cis-prenyl-transferases that may be useful as herbicides or fungicides. This could be achieved either through the rational design and synthesis of potent functional inhibitors that result from structural and/or mechanistic information that is derived from the purified instant plant proteins, or through random in vitro screening of chemical libraries. It is anticipated that significant in vivo inhibition of the cis-prenyltransferase proteins described herein may severely cripple cellular metabolism and likely result in plant (or fungal) death.

All or a portion of the nucleic acid fragments of the instant invention may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to expression of the instant cis-prenyltransferases. Such information may be useful in plant breeding in order to develop lines with desired phenotypes. For example, the instant nucleic acid fragments may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Maniatus, supra) of restriction-digested plant genomic DNA may be probed with the nucleic acid fragments of the instant invention. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al., Genomics 1:174-181 (1987)) in order to construct a genetic map. In addition, the nucleic acid fragments of the instant invention may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the instant nucleic acid sequences in the genetic map previously obtained using this population (Botstein et al., Am. J. Hum. Genet. 32:314-331 (1980)).

The production and use of plant gene-derived probes for use in genetic mapping is described by Bernatzky et al. (Plant Mol. Biol. Reporter 4:37-41 (1986)). Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.

Nucleic acid probes derived from the instant nucleic acid sequences may also be used for physical mapping (i.e., placement of sequences on physical maps; see Hoheisel et al., Nonmammalian Genomic Analysis: A Practical Guide; Academic, 1996; pp. 319-346 and references cited therein).

In another embodiment, nucleic acid probes derived from the instant nucleic acid sequences may be used in direct fluorescence in situ hybridization (FISH) mapping. Although current methods of FISH mapping favor use of large clones, improvements in sensitivity may allow performance of FISH mapping using shorter probes.

A variety of nucleic acid amplification-based methods of genetic and physical mapping may be carried out using the instant nucleic acid sequences. Examples include allele-specific amplification (Kazazian et al., J. Lab. Clin. Med. 114:95-96 (1989)), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al., Genomics 16:325-332 (1993)), allele-specific ligation (Landegren et al., Science 241:1077-1080 (1988)), nucleotide extension reactions (Sokolov et al., Nucleic Acid Res. 18:3671 (1990)), Radiation Hybrid Mapping (Walter et al., Nature Genetics 7:22-28 (1997)), and Happy Mapping (Dear et al., Nucleic Acid Res. 17:6795-6807 (1989)). For these methods, the sequence of a nucleic acid fragment is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods using PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods.

Loss of function-mutant phenotypes may be identified for the instant cDNA clone either by targeted gene disruption protocols or by ideritifying specific mutants for this gene contained in a population of plants carrying mutations in all possible genes (e.g., Ballinger et al., Proc. Natl. Acad. Sci. USA 86:9402 (1989); Koes et al., Proc. Natl. Acad. Sci. USA 92:8149 (1995); Bensen et al., Plant Cell 7:75 (1995)). The latter approach may be accomplished in two ways. First, short segments of the instant nucleic acid fragments may be used in polymerase chain reaction protocols in conjunction with a mutation tag sequence primer on DNAs prepared from a population of plants in which Mutator transposons or some other mutation-causing DNA element has been introduced (see Bensen et al., supra). The amplification of a specific DNA fragment with these primers indicates the insertion of the mutation tag element in or near the plant gene encoding the cis-prenyltransferase protein. Alternatively, the instant nucleic acid fragments may be used as a hybridization probe against PCR amplification products generated from the mutation population using the mutation tag sequence primer in conjunction with an arbitrary genomic site primer, such as that for a restriction enzyme site-anchored synthetic adaptor. With either method, a plant containing a mutation in the endogenous gene encoding a cis-prenyltransferase protein can be identified and obtained. This mutant plant can then be used to determine or confirm the natural function of the cis-prenyltransferase gene product.

DESCRIPTION OF PREFERRED EMBODIMENTS

Numerous studies have examined prenyltransferases capable producing long-chain isoprenoids with trans-chain configuration. However, identification of those prenyltransferases that condense isoprene units in the cis-configuration are less well studied. Undecaprenyl pyrophosphate synthetase (di-trans,poly-cis-decaprenylcistransferase, or Upp synthetase; EC 2.5.1.31) was first isolated from E. coli in 1999 by Apfel et al. (J. Bact. 181(2): 483-492). Apfel et al. also published an alignment of the deduced amino acid sequence of the E. coli Upp synthase gene with a number (28) of other publicly-available sequences from bacteria, yeast (Saccharomyces cerevisiae) and one eukaryote (Caenorhabditis elegans), which revealed five conserved domains. These domains are shown below: (SEQ ID NO:29) Domain I: HxxxxMDGN(RG)R(WYF)A; (SEQ ID NO:30) Domain II: GHxxG; (SEQ ID NO:31) Domain III: (TS)xxAFS(ST)ENxxRxxxEVxxLMxL; (SEQ ID NO:32) Domain IV: AxxYGGRx(DE)(LIVM)xxA; (SEQ ID NO:33) Domain V: (DE)LxIRT(SAG)GExRxSNF(ML)(LMP)WQxxY (SAT)ExxFxxxxWP(DE)F.

Apfel et al. predicts that these conserved domains, as well as a few single conserved amino acids outside of the conserved domains, likely represent the active site of the protein.

In the present invention, the Applicants describe unique plant homologs of microbial cis-prenyltransferase proteins that are involved in the synthesis of poly-cis-isoprenoids. More specifically, these cis-prenyltransferases have been isolated from the natural rubber producing plants russian dandelion (Taraxacum kok-saghyz) and sunflower (Helianthus annus). Comparison of these cDNA sequences to the GenBank database using the BLAST algorithm, well known to those skilled in the art, reveals that these cis-prenyltransferase proteins belong to the broad family of known cis-prenyltransferase genes. This conclusion is additionally based on the presence of conserved domains I-V, as described by Apfel et al., supra.

Further analysis of cis-prenyltransferase sequences, however, reveals surprisingly unique characteristics that are specific for those cis-prenyltransferases isolated from rubber-producing plants. More specifically, the Applicants describe:

-   -   1. Modified sequences of conserved domains I, IV, and V, with         respect to Apfel et al., that are indicative of the subfamily of         cis-prenyltransferases associated with rubber-producing plants;         and     -   2. A unique non-conserved domain between conserved domain IV and         V, that is present in cis-prenyltransferases from         rubber-producing plants and that is absent in         cis-prenyltransferases from other plants.

These two identifying characteristics are thus diagnostic for cis-prenyltransferases from rubber-producing plants and will permit rapid identification of cis-prenyltransferases from rubber-producing species.

EXAMPLES

The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various usages and conditions.

GENERAL METHODS

Standard recombinant DNA and molecular cloning techniques used here are well known in the art and are described by Sambrook et al., Molecular Cloning: A Laboratory Manual, 2^(nd) ed., Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1989 (hereinafter “Maniatus”); and by T. J. Silhavy, M. L. Bennan, and L. W. Enquist, Experiments with Gene Fusions, Cold Spring Harbor Laboratory: Cold Spring Harbor, N.Y., 1984; and by Ausubel et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience, 1987. Nucleotide and amino acid percent identity and similarity comparisons were made using the BLAST (Basic Local Alignment Search Tool; Altschul et al., J. Mol. Biol. 215:403-410 (1993); see also www.ncbi.nlm.nih.gov/BLAST/) algorithms and also the Vector NTI suite of programs, applying default parameters unless indicated otherwise. The meaning of abbreviations is as follows: “sec” means second(s), “min” means minute(s), “h” means hour(s), “d” means day(s), “μL” means microliter, “mL” means milliliters, “L” means liters, “μM” means micromolar, “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “μmole” mean micromole”, “g” means gram, “μg” means microgram, “ng” means nanogram, “U” means units, “bp” means base pairs, and “kB” means kilobase.

Example 1 Preparation of cDNA Libraries from Russian Dandelion and Sunflower

This example describes the preparation of two cDNA libraries, one from russian dandelion latex tissue and one from sunflower leaf tissue. These libraries were then used for sequencing of expressed sequencing tags (ESTs).

Library Construction for Russian Dandelion, Taraxacum kok-saqhyz

A cDNA library representing mRNAs from russian dandelion latex tissue was prepared, using the SMART cDNA Library Construction Kit (Clontech, Palo Alto, Calif.). The cDNAs were introduced into plasmid vectors by first preparing the cDNA library in λTriplEx2 vectors and then converted into a plasmid library (Clontech). Upon conversion, cDNA inserts were contained in the plasmid vector pTriplEx2 and plasmid DNAs were prepared from randomly selected bacterial colonies. Amplified insert DNAs or plasmid DNAs were sequenced in dye-primer sequencing reactions to generate partial cDNA sequences (expressed sequence tags or “ESTs”; see Adams et al., Science 252:1651-1656 (1991)). The resulting ESTs were analyzed using a Perkin Elmer Model 377 fluorescent sequencer.

Library Construction for Sunflower, Helianthus annus

SMF3 Sunflower plants were grown in the greenhouse for 4 weeks and then transferred to a growth chamber with a 12 hr photoperiod, at 22° C. and 80% relative humidity. The sunflower pathogen, Schlerotinia sclerotiorum (isolate 255M), was maintained on a PDA plate at 20° C. in the dark. When the sunflower plants were 6 weeks old, they were inoculated with Sclerotinia-infested carrot plugs with active growing mycelia. For each plant, three petioles were inoculated and wrapped with parafilm. Leaf tissue samples were collected, immediately frozen in liquid nitrogen, and stored at −80° C.

Total RNA was isolated from this tissue using TriPure Reagent (Roche Applied Science, Indianapolis, Ind.). Subsequently, mRNAs were isolated using a mRNA purification kit (Invitrogen, Carlsbad, Calif.). A cDNA library representing mRNAs from sunflower leaf tissue infected with the pathogen S. scierotiorum was prepared, using the Lamda ZAPII-cDNA synthesis kit (Stratagene, LaJolla, Calif.). Once the cDNA inserts were in plasmid vectors, plasmid DNAs were prepared from randomly selected bacterial colonies containing recombinant pBluescript plasmids. Amplified insert DNAs or plasmid DNAs were sequenced in dye-primer sequencing reactions to generate partial cDNA sequences (expressed sequence tags or “ESTs”; see Adams et al., supra. The resulting ESTs were analyzed using a Perkin Elmer Model 377 fluorescent sequencer.

Example 2 Identification and Characterization of cis-Prenvitransferases

This Example describes the methodology utilized to conduct BLAST analyses on each EST sequenced in Example 1 and the identification of two novel cis-prenyltransferase genes.

Specifically, all sequences from Example 1 were identified by conducting BLAST (Basic Local Alignment Search Tool; Altschul, S. F., et al., (1993) J. Mol. Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences contained in the BLAST “nr” database (comprising all non-redundant GenBank CDS translations, sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank, the SWISS-PROT protein sequence database, EMBL, and DDBJ databases).

The cDNA sequences were analyzed for similarity to all publicly available DNA sequences contained in the “nr” database using the BLASTN algorithm provided by the National Center for Biotechnology Information (NCBI). The DNA sequences were translated in all reading frames and compared for similarity to all publicly available protein sequences contained in the “nr” database using the BLASTX algorithm (Gish, W. and States, D. J. Nature Genetics 3:266-272 (1993)) provided by the NCBI.

cDNAs were further identified by searches of the database using the TBLASTN algorithm provided by the National Center for Biotechnology Information (NCBI) and short fragments of conserved sequence present in known cis-prenyltransferases (conserved domains I-V, as described by .Apfel et al., J. Bacteriol. 81:483-492 (1999)). These sections of conserved sequence were expected to be diagnostic for the cis-prenyltransferase family of enzymes.

The results of these BLAST comparisons are given below in Table 2 for the ESTs of the present invention. Table 2 summarizes the sequence to which each EST potentially encoding a cis-prenyltransferase has the most similarity (presented as % similarities, % identities, and expectation values). The table displays data based on the BLASTXnr algorithm with values reported in expect values. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected in a search of a database of this size absolutely by chance. TABLE 2 ESTs Potentially Encoding Cis-Prenyltransferases, as Identified by Automated BLAST Searches of Public Databases EST SEQ ORF and Organism of ID % % Name Isolation Similarity Identified NOs Identity^(a) Similarity^(b) E-value^(c) Citation 1 Cis- H. brasiliensis cis- 1, 2 44 64 4.4 × 10⁻²⁰ Asawatreratanakul, K., prenyltransferase prenyltransferase Zhang, Y. W., etk1c.pk006.a10 (hcpt-3 mRNA, Wititsuwannakul, R. and (Taraxacum kok- partial cds) Koyama, T., direct saghyz) (AB061235) submission 2 Cis- H. brasiliensis cis- 5, 6 57 81 2.0 × 10⁻³² Asawatreratanakul, K., prenyltransferase prenyltransferase Zhang, Y. W., hls1c.pk020.m9 (AB061237) Wititsuwannakul, R. and (Helianthus Koyama, T., direct annus) submission ^(a)% Identity is defined as percentage of amino acids that are identical between the two proteins. ^(b)% Similarity is defined as percentage of amino acids that are identical or conserved between the two proteins. ^(c)Expect value. The Expect value estimates the statistical significance of the match, specifying the number of matches, with a given score, that are expected in a search of a database of this size absolutely by chance.

The russian dandelion EST was found to have the highest homology (44% identity) to a partial clone of a cis-prehyltransferase gene of H. brasiliensis (Accession Number AB061235), using automated BLAST searches against sequences deposited in the public databases (Table 2). To further analyze the dandelion EST sequence, it was translated and aligned with other full-length cis-prenyltransferase genes. Using this approach the sequence exhibited 30.5% identity with its closest homolog, the Hevea Hpt1 gene product (SEQ ID NO:8)

The sunflower EST sequence was found to have the highest homology (57% identity) to a full-length clone of a cis-prenyltransferase gene of H. brasiliensis (Accession Number AB061237), using automated BLAST searches against sequences deposited in the public databases (Table 2). Comparison of the sunflower EST sequence (SEQ ID NO:6) to the Hevea Hpt1 gene product (SEQ ID NO:8) determined that there was 24.4% identity to Hpt1.

In addition to the homology both ESTs exhibited with other known cis-prenyltransferase genes, the russian dandelion and sunflower EST also was found to possess significant homology to one of the five conserved domains reported by Apfel et al. (supra). Specifically, both ESTs possesed the amino acid sequence: DILVRSSGETRLSNFLLWQTTNCVLYSPKALWPEM (SEQ ID NO: 34), which shares homology with Domain V of Apfel et al. (supra).

Further analysis of the DNA alignments, however, revealed that both the russian dandelion and sunflower EST sequences did not encode full length ORFs. The 5′ end of the russian dandelion cDNA appeared to be missing over 201 bp, while the sunflower cDNA appeared to be missing over 192 bp of its 5′ sequence. The full-length cis-prenyltransferase cDNA sequences, therefore, could not be determined, and the low % homologies in alignments with known cis-prenyltransferases are due to use of partial cDNAs.

Example 3 Acquisition of Full-length Russian Dandelion Cis-prenyltransferase cDNA

This Example describes the methodology used to isolate the full-length cDNA for the russian dandelion cis-prenyltranferase, since the dandelion sequence analyzed in Example 2 appeared to be missing the 5′ end when aligned with known full-length cis-prenyltransferases.

Rapid amplification of cDNA ends (RACE) was performed to obtain the 5′ end sequence of the russian dandelion cis-prenyltransferase gene, using the FirstChoice RLM-RACE Kit (Ambion, Austin, Tex.). The gene-specific oligonucleotides used for the outer 5′RLM-RACE PCR was NKH46 (SEQ ID NO:36) and for the inner 5′RLM-RACE PCR was NKH45 (SEQ ID NO:37). Several PCR products were obtained by RACE. These products were then cloned using a TOPO TA-cloning kit (Invitrogen, Carlsbad, Calif.) and transformed into E. coli. Plasmids were isolated and purified using QIAFilter cartridges (Qiagen, Valencia, Calif.).

Sequences were generated on an ABI Automatic sequencer using dye terminator technology, using a combination of vector-specific primers, and editing was performed in Vector NTI (InforMax Inc., North Bethesda, Md.). To aid in the analysis of RACE PCR products, the design of the primers used in RACE was such that the amplified 5′ end RACE products contain at least 200 bp from the 5′ end of the known partial cDNA sequence. Thus, the sequence of the PCR products obtained by RACE were aligned with the cDNA sequence of the russian dandelion cis-prenyltransferase EST in Vector NTI's Contig Express. Those PCR products that did not align with at least 200 bp of the partial cDNA sequence of the russian dandelion cis-prenyltransferase EST were discarded. One clone (#3-4) obtained by 5′ RACE contained 258 bp of sequence (SEQ ID NO:2) identical to that of the EST representing the partial russian dandelion cis-prenyltransferase cDNA, verifying that this RACE product was genuine. This allowed the sequence of the full-length russian dandelion cDNA clone (SEQ ID NO:3) to be assembled in Vector NTI's ContigExpress program. The deduced full-length amino acid sequence (SEQ ID NO:4) exhibited 49.8% identity (61.2% similarity) with that of the Hevea Hpt1 gene product (SEQ ID NO:8).

Example 4 Identification of a Diagnostic Non-Conserved Domain in Rubber-Producing cis-Prenyltransferases

This Example describes the identification of a non-conserved domain in the cis-prenyltransferases of rubber-producing plants, discovered from alignments of three Hevea cis-prenyltransferases (SEQ ID NOs:8-10), the russian dandelion cis-prenyltransferase (SEQ ID NO:4), and the sunflower cis-prenyltransferase (SEQ ID NO:6). This domain will be a useful tool to rapidly identify cis-prenyltransferases likely to be involved in long-chain rubber biosynthesis in the future. Additionally, modified conserved domains were identified for cis-prenyltransferases from rubber-producing plant species, corresponding to the conserved domains of Apfel et al. (J. Bacteriol. 81:483-492 (1999)).

An alignment of the deduced amino acid sequences of the cDNAs of the instant invention with various known cis-prenyltransferases (WO 01/21650) was created, using the CLUSTALW program within the VECTOR NTI suite of programs (full alignment not shown). Specifically, aligned sequences include those from: 1.) rubber-producing plants (i.e., russian dandelion, sunflower and Hevea, corresponding to SEQ ID NOs:4, 6 and 8-10); 2.) non-rubber-producing plants (i.e., rice, marigold, grape, soybean, wheat, African daisy, and Arabidopsis, corresponding to SEQ ID NOs:12, 7, 11, 14, 15, 16, and 23-26); and 3.) microbes (i.e., Micrococcus and Saccharomyces, corresponding to SEQ ID NOs:18 and 20 and 22). The alignment confirmed the presence of the conserved domains characteristic of this gene family (Apfel et al., supra).

A portion of the alignment is shown in FIG. 1, corresponding to the region between Domain IV and V. This region defines a non-conserved domain indicative of the subfamily of cis-prenyltransferases associated with rubber-producing plants. Specifically, the domain comprises a sequence of non-conserved amino acids present between Domains IV and V, wherein the presence of the domain results in more than 50 amino acid residues being present between the absolutely conserved tyrosine of Domain IV and the first of the absolutely conserved arginine residues of Domain V. This is the first sequence feature to emerge as diagnostic for cis-prenyltransferases from rubber-producing plants, as there had not been enough proteins from such species characterized prior to this discovery to be able to identify such distinguishing feature(s).

Interestingly, SEQ ID NO:24, an Arabidopsis cis-prenyltransferase genomic clone of unknown function, alone of the non-rubber-producing species, contains a similar insert to the identified non-conserved domain of the present invention. This gene in Arabidopsis may thus represent a homolog of cis-prenyltransferases involved in rubber production present in the genome of this species.

Additionally, a cis-prenyltransferase protein from a rubber-producing plant can be identified by the presence of the conserved domains of amino acid sequences as follows: (SEQ ID NO:38) Domain I AFI(L/M)DGNRRFA (SEQ ID NO:39) Domain IV Y(T/S)SXX(D/E)IXXA (SEQ ID NO:40) Domain V PXPD(I/V)L(I/V)R(S/T)SG(E/L)(S/T) RLSNXLLWQ where these three domains occur sequentially in the order I, IV, V within the amino acid sequence and X may be any amino acid. These domains are essentially those recognized previously in bacterial sequences (Apfel, et al. supra), but have been modified to account for the differences observed in alignments of sequences of cis-prenyltransferases derived from plants (WO 01/21650).

Example 5 Expression Analysis of the Russian Dandelion cis-prenyltransferase

This example describes work performed to examine the expression of the russian dandelion cis-prenyltransferase in leaf, root, scape and latex tissues. As expected, the protein is expressed predominantly in tissues known to accumulate rubber in this species (i.e., in the rubber-containing latex).

RNA was prepared from the leaf, root and scape of russian dandelion, using the RNAeasy Midi-Kit (Qiagen, Valencia, Calif.) for samples from plant tissue. RNA from russian dandelion latex was prepared as decribed by Kush, et. al. (Proc. Natl. Acad. Sci. 87:1787-1790 (1990)). 10 μg of total RNA from russian dandelion latex, leaf, root, and scape was denatured on a formadelhyde gel, using products and the supplied protocol from 5′ to 3′, Inc. (Boulder, Colo.). The gel was rinsed twice in 20×SSC for 15 min and then transferred to a nylon membrane (Roche Applied Science, Indianapolis, Ind.) by capillary action at 4° C. overnight. The RNA was then crosslinked to the membrane using a UV crosslinker (Stratagene, La Jolla, Calif.).

A digoxigenin (DIG) labeled russian dandelion cis-prenyltransferase EST fragment was synthesized, using the PCR DIG Probe Synthesis Kit (Roche Applied Science, Indianapolis, Ind.) and the following oligionucleotides: Dan5 (SEQ ID NO:41) and Dan6 (SEQ ID NO:42). This probe was then hybridized to the membrane and detected using the DIG Wash and Block Buffer Set (Roche Applied Science, Indianapolis, Ind.). The membrane was then exposed to BioMax Scientific Imaging Film (Eastman Kodak Co., Rochester, N.Y.) for 20 min. As shown in FIG. 2A, cis-prenyltransferase expression was detected in the root (lane A), scape (lane B) and latex (lane C) tissues, with the highest level of expression detected in latex. Little or no expression of cis-prenyltransferase was detected in the leaf tissue (lane D).

The membrane was then stripped of the DIG labeled russian dandelion cis-prenyltransferase probe by washing it in boiling 0.1% SDS for 10 min, followed by 1× Washing Buffer from the DIG Wash and Block Buffer Set for 5 min. A digoxigenin (DIG) labeled russian dandelion ubiquitin probe was synthesized, using the DIG DNA labeling Kit, according to the supplied protocol (Roche Applied Science). This probe was then hybridized to the membrane, detected using the DIG Wash and Block Buffer Set, and the membrane was exposed to BioMax Scientific Imaging Film (20 min).

Ubiquitin expression was detected in all tissues (FIG. 2B). Assuming that ubiquitin is equally expressed in all russian dandelion tissues, the amount of leaf (lane D), latex (lane C) and root (lane A) RNA loaded onto the gel was approximately equal while slightly more scape (lane B) RNA was loaded. It is clear from this analysis that the dandelion cis-prenyltransferase gene is expressed predominantly in tissues known to accumulate rubber in this species, and in particular in the rubber-containing latex. Thus, there is a clear association between this gene product and rubber biosynthesis.

Example 6 Cloning of a Partial cDNA Sequence of the Russian Dandelion cis-prenyltransferase gene Using Synthetic Oligonucleotide Primers in Reverse-transcriptase PCR

This Example serves to confirm the presence of a transcript of the cloned cis-prenyltransferase gene in latex of russian dandelion, as indicated in the proceeding examples. It also demonstrates how synthetic oligonucleotide primers designed using gene sequences of plant cis-prenyltransferases may be used to clone additional cis-prenyltransferase genes from other species.

SEQ ID NOs:8-10, respresenting the Hevea Hpt1, Hpt2 and Hpt3 proteins were aligned using Vector NTI. A degenerate sense primer was designed to a region of high conservation (SEQ ID NO:43). Then, the following amino acid sequences were aligned in Vector NTI: SEQ ID NOs:7-10 and 12-16, representing the cis-prenyltransferase proteins from Hevea, pot marigold, rice, soybean, wheat, and the african daisy. A degenerate antisense primer was designed to a region of high conservation (SEQ ID NO:44).

RT-PCR was performed on total russian dandelion latex RNA with these primers (SEQ ID NOs:43 and 44), using Platinum PCR SuperMix (Invitrogen, Carlsbad, Calif.). The resulting RT-PCR products were TA-cloned, using the pGEM-t Easy Vector System (Promega Corp., Madison, Wis.) and the resulting plasmids were transformed into E. coli. Plasmids were isolated and purified using QIAFilter cartridges (Qiagen, Valencia, Calif.). Sequences were generated on an ABI Automatic sequencer using dye terminator technology, using a combination of vector-specific primers, and sequence editing was performed in Vector NTI.

The nucleotide sequences of the RT-PCR products were aligned with nucleotide sequences of known plant cis-prenyltransferase genes (Table 1). One 799 bp RT-PCR product (clone #4-4) showed significant homology to the known cis-prenyltransferase genes. The deduced amino acid sequence of this RT-PCR product (SEQ ID NO:45) was aligned with the deduced amino acid sequences of the known plant cis-prenyltransferase proteins as well as the amino acid sequence of the undecaprenyl diphosphate synthase (UPPS) protein and was determined by homology to be a russian dandelion homolog of UPPS.

Example 7 Comparison of Rubbers Prepared from Different Rubber-producing Plant Species

This Example compares the properties of natural rubber prepared from russian dandelion, Hevea, sunflower and guayule.

The roots of 5 russian dandelion plants were cut off at the point where leaves emerged, and latex which seeped out of the cut roots was collected, yielding 200 mg latex. After stirring overnight in toluene (10 ml), the preparation was extracted with water in a separating funnel and the rubber precipitated from the organic phase by addition of an equal volume of methanol. After redissolving in toluene, methanol precipitation was repeated a further two times to purify the rubber. A total of 49.3 mg rubber was thus obtained, which was dissolved in toluene for analysis.

Hevea and guayule (P. argentatum) washed rubber particles were prepared essentially according to previously published procedures (Comish, K., et al. J. Natural Rubber Res. 8:275-285 (1993); Cornish, K., and Backhaus, R. Phytochemistry 29: 3808-3813 (1990)). Rubber was extracted into toluene and, after washing with water, precipitated three times with methanol as described above. From 274 mg guayule rubber particles, 45.6 mg rubber was obtained; and from 303.8 mg Hevea rubber particles, 50.8 mg rubber was obtained.

Sunflower rubber was prepared by extraction of freeze-dried leaf material in a Soxhlet apparatus first with acetone and then with hexane. To the hexane extract, an equal volume of methanol was added to precipitate the rubber. The precipitate was collected by filtration onto glass fiber filters, and after allowing solvent to evaporate, redissolved in toluene. Methanol precipitation from toluene was repeated three times. From 27.7 g leaf dry weight, 5.1 mg rubber was obtained.

To determine molecular weight, samples of rubber (dissolved in toluene) were subjected to gel permeation chromatography on PLGel columns (Polymer Laboratories, Amherst, Mass.) calibrated with polystyrene standards (Polymer Laboratories). Tetrahydrofuran (THF) was used as eluent, and refractive index and UV absorbtion were monitored.

Data obtained from these analyses (Table 3) show that rubber extracted from these 4 species exhibit marked differences in molecular weight and molecular weight distribution (MWD), or polydispersity. The large degree of polydispersity in the rubber of Hevea is due to the presence of two distinct peaks in the chromatogram, as has previously been observed (Subramanian, A. Gel Permeation Chromatography of Natural Rubber. In, Rubber Chemistry & Technology March 1972; pp. 346-358). In contrast, the rubbers of russian dandelion, sunflower and guayule are monodisperse.

The rubber obtained from russian dandelion exhibited a higher weight average molecular weight (MW) than that of Hevea, while sunflower rubber was of considerably lower molecular weight, in accordance with previous observations (Seiler, G. J., et al., Economic Botany 45: 4-15 (1991)). This molecular weight of sunflower is close to the molecular weight desired for an ‘ideal’ liquid natural rubber (LNR), which would have the following properties (Nor, H. M., and Ebdon, J. R. Progress in Polymer Science 23: 143-177 (1998)):

-   -   A weight average molecular weight (Mw) of <80,000;     -   A number average molecular weight (Mn) of <50,000;     -   A MWD (determined as Mw/Mn) of <4.0; and

An intrinsic viscosity (IV) of 0.2-0.5. TABLE 3 Gel Permeation Chromatography analysis of plant rubbers PLANT SPECIES MW¹ MN² MWD³ IV⁴ H. brasiliensis 1.44 × 10⁶ 252,689 5.71 7.35 H. annus 68,998  33,134 2.08 0.671 P. argentatum 1.47 × 10⁶ 641,640 2.3 7.719 T. kok-saghyz 2.18 × 10⁶ 1.21 × 10⁶ 1.8 10.633 ¹Weight average molecular weight ²Number average molecular weight ³MW/MN ⁴Intrinsic viscosity

As expected from previous studies, different rubbers from different species can display marked differences in their fundamental properties of molecular weight, polydispersity, and intrinsic velocity. These factors must be considered during the development of alternative commercial rubber sources to Hevea, and are likely to be influenced by the specific cis-prenyltransferase enzymes involved in their polymerization. 

1. An isolated nucleic acid molecule encoding a cis-prenyltransferase enzyme, selected from the group consisting of: a) an isolated nucleic acid molecule encoding the amino acid sequence as set forth in SEQ ID NOs:4 and 6; b) an isolated nucleic acid molecule that hybridizes with (a) under the following hybridization conditions: 0.1×SSC, 0.1% SDS, 65° C. and washed with 2×SSC, 0.1% SDS followed by 0.1×SSC, 0.1% SDS; or an isolated nucleic acid molecule that is complementary to (a) or (b).
 2. An isolated nucleic acid molecule as set forth in SEQ ID NOs: 3 and
 5. 3. A polypeptide encoded by the isolated nucleic acid molecule of claim
 1. 4. A polypeptide encoded by the isolated nucleic acid molecule of claim
 2. 5. A polypeptide having the amino acid sequence selected from the group consisting of SEQ ID NO:4 and SEQ ID NO:6.
 6. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 301 amino acids that has at least 70% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO:4 or a second nucleotide sequence comprising the complement of the first nucleotide sequence, wherein said enzyme has cis-prenyltransferase activity.
 7. An isolated nucleic acid molecule comprising a first nucleotide sequence encoding a polypeptide of at least 168 amino acids that has at least 70% identity based on the Smith-Waterman method of alignment when compared to a polypeptide having the sequence as set forth in SEQ ID NO:6 or a second nucleotide sequence comprising the complement of the first nucleotide sequence, wherein said enzyme has cis-prenyltransferase activity.
 8. A chimeric gene comprising the isolated nucleic acid molecule of claim 1 operably linked to suitable regulatory sequences.
 9. A transformed host cell comprising the chimeric gene of claim
 8. 10. The transformed host cell of claim 9 wherein the host cell is selected from the group consisting of plant cells and microbial cells.
 11. A host cell according to claim 10 selected from the group consisting of russian dandelion (Taraxacum kok-saghyz), rubber tree (Hevea brasiliensis), guayule (Parthenium argentatum), sunflower (Helianthus spp.), tobacco (Nicotiana spp.), tomato (Lycopersicon spp.), potato (Solanum spp.), hemp (Cannabis spp.), sorghum (Sorghum vulgare), wheat (Triticum spp.), maize (Zea mays), rice (Oryza sativa), rye (Secale cereale), oats (Avena spp.), barley (Hordeum vulgare), rapeseed (Brassica spp.), broad bean (Vicia faba), french bean (Phaseolus vulgaris), other bean species (Vigna spp.), lentil (Lens culinaris), soybean (Glycine max), arabidopsis (Arabidopsis thaliana), cofton (Gossypium hirsutum), petunia (Petunia hybrida), flax (Linum usitatissimum) and carrot (Daucus carota sativa).
 12. The transformed host cell of claim 10 wherein the host cell is selected from the group consisting of Aspergillus, Saccharomyces, Pichia, Candida, Hansenula, Bacillus, Escherichia, Salmonella and Shigella.
 13. A method of obtaining a nucleic acid molecule encoding a cis-prenyltransferase enzyme comprising: a) probing a genomic library with the nucleic acid molecule of claim 1; b) identifying a DNA clone that hybridizes with the nucleic acid molecule of claim 1; and c) sequencing the genomic fragment that comprises the clone identified in step (b), wherein the sequenced genomic fragment encodes a cis-prenyltransferase enzyme.
 14. A method of obtaining a nucleic acid molecule encoding a cis-prenyltransferase enzyme comprising: a) synthesizing at least one oligonucleotide primer corresponding to a portion of the sequence selected from the group consisting of SEQ ID NOs:3 and 5; and b) amplifying an insert present in a cloning vector using the oligonucleotide primer of step (a); wherein the amplified insert encodes a portion of an amino acid sequence encoding a cis-prenyltransferase enzyme.
 15. The product of the method of claims 13 or
 14. 16. A method of altering the level of expression of a plant cis-prenyltransferase protein in a host cell comprising: (a) transforming a host cell with the chimeric gene of claim 8 and; (b) growing the transformed host cell produced in step (a) under conditions that are suitable for expression of the chimeric gene resulting in production of altered levels of a plant cis-prenyltransferase protein in the transformed host cell relative to expression levels of an untransformed host cell.
 17. A method according to claim 16 wherein the method of altering the level of expression of a plant cis-prenyltransferase protein in a host cell comprises over-expressing at least one cis-prenyltransferase gene selected from the group consisting of SEQ ID NOs: 3 and
 5. 18. A method according to claim 16 wherein the method of altering the level of expression of a plant cis-prenyltransferase protein in a host cell comprises over-expressing the cis-prenyltransferase gene on a multicopy plasmid.
 19. A method according to claim 16 wherein said chimeric gene is operably linked to an inducible or regulated promoter.
 20. A method according to claim 16 wherein chimeric gene is expressed in antisense orientation.
 21. A method according to claim 16 wherein said chimeric gene is disrupted by insertion of foreign DNA into the coding region.
 22. A method according to claim 16 wherein the altering the level of expression of a plant cis-prenyltransferase protein results in a modulation in the defense mechanism of the plant.
 23. A method for the production of natural rubber compounds comprising: a) providing a transformed host cell comprising: (i) suitable levels of isopentenyl pyrophate; and (ii) a cis-prenyltransferase gene selected from the group consisting of SEQ ID NOs: 3 and 5, wherein said genes are operably linked to suitable regulatory sequences; and b) growing the transformed host cell of (a) under conditions whereby a natural rubber compound is produced.
 24. A method for the identification of a polypeptide having cis-prenyltransferase activity in a rubber-producing plant comprising: (a) obtaining the amino acid sequence of a polypeptide suspected of having cis-prenyltransferase activity; and (b) aligning the amino acid sequence of step (a) with the amino acid sequence of a cis-prenyltransferase consensus sequence selected from the group consisting of SEQ ID NO:4, 6, 8, 9, and 10, wherein the alignment shows the presence of conserved domains I, IV, and V (SEQ ID NOs: 38-40).
 25. A method for the identification of a polypeptide having cis-prenyltransferase activity in a rubber-producing plant comprising: (a) obtaining the amino acid sequence of a polypeptide suspected of having cis-prenyltransferase activity; and (b) aligning the amino acid sequence of step (a) with the amino acid sequence of a cis-prenyltransferase consensus sequence selected from the group consisting of SEQ ID NO:4, 6, 8, 9, and 10, wherein the alignment shows a sequence of at least about 50 non-conserved amino acids present between the absolutely conserved tyrosine of Domain IV and the first of the absolutely conserved arginine residue of Domain V. 